*/
package MCview;
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Event;
import java.util.List;
import java.util.Vector;
-import jalview.analysis.AlignSeq;
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.FeatureRenderer;
-import jalview.appletgui.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
public class AppletPDBCanvas extends Panel implements MouseListener,
MouseMotionListener, StructureListener
{
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.chains.elementAt(i).sequence
- .getSequenceAsString());
+ + pdb.chains.elementAt(i).sequence.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + pdb.chains.elementAt(i).residues.size()
- + "\n\n");
+ + pdb.chains.elementAt(i).residues.size() + "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
pdb.chains.elementAt(i).sequence,
- pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
// /StructureListener
public String[] getPdbFile()
{
- return new String[]
- { pdbentry.getFile() };
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
*/
package MCview;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.CheckboxGroup;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
public class AppletPDBViewer extends EmbmenuFrame implements
ActionListener, ItemListener
{
public Bond(Atom at1, Atom at2)
{
- this.start = new float[]
- { at1.x, at1.y, at1.z };
- this.end = new float[]
- { at2.x, at2.y, at2.z };
+ this.start = new float[] { at1.x, at1.y, at1.z };
+ this.end = new float[] { at2.x, at2.y, at2.z };
this.startCol = at1.color;
this.endCol = at2.color;
this.at1 = at1;
*/
package MCview;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Event;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
public class PDBCanvas extends JPanel implements MouseListener,
MouseMotionListener, StructureListener
{
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.chains.elementAt(i).sequence
- .getSequenceAsString());
+ + pdb.chains.elementAt(i).sequence.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + pdb.chains.elementAt(i).residues.size()
- + "\n\n");
+ + pdb.chains.elementAt(i).residues.size() + "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// /StructureListener
public String[] getPdbFile()
{
- return new String[]
- { pdbentry.getFile() };
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
*/
package MCview;
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
if (features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 + residues.elementAt(tx.getBegin()
- - offset).atoms.elementAt(0).alignmentMapping);
- tx.setEnd(1 + residues.elementAt(tx.getEnd()
- - offset).atoms.elementAt(0).alignmentMapping);
+ tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping);
+ tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping);
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
"Temperature Factor", "Temperature Factor for " + pdbid + id,
- annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
+ annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
{
try
{
- index = ResidueProperties.aa3Hash.get(b.at1.resName)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- index = ResidueProperties.aa3Hash.get(b.at2.resName)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
} catch (Exception e)
* @param sqmpping
* - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(
- StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
+ public void transferResidueAnnotation(StructureMapping mapping,
+ jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
}
});
viewMenu.setText(MessageManager.getString("action.view"));
- background.setText(MessageManager.getString("action.background_colour"));
+ background
+ .setText(MessageManager.getString("action.background_colour"));
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
- "Make PNG image from view", width, height, null, null);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle());
}
else
{
*/
private boolean externalSecondaryStructure = false;
- public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
- boolean externalSecStr)
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
{
super();
this.visibleChainAnnotation = addAlignmentAnnotations;
this.externalSecondaryStructure = externalSecStr;
}
- public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
- boolean externalSecStr, String file, String protocol)
- throws IOException
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
{
super(false, file, protocol);
this.visibleChainAnnotation = addAlignmentAnnotations;
doParse();
}
- public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
- boolean externalSecStr, FileParse source) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
{
super(false, source);
this.visibleChainAnnotation = addAlignmentAnnotations;
processPdbFileWithAnnotate3d(rnaSequences);
} catch (Exception x)
{
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
+ System.err.println("Exceptions when dealing with RNA in pdb file");
x.printStackTrace();
}
public static String relocateCalcId(String calcId,
Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- int s = CALC_ID_PREFIX.length(), end = calcId.indexOf(CALC_ID_PREFIX, s);
+ int s = CALC_ID_PREFIX.length(), end = calcId
+ .indexOf(CALC_ID_PREFIX, s);
String between = calcId.substring(s, end - 1);
return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ calcId.substring(end);
Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
if (cl != null)
{
- final Constructor constructor = cl.getConstructor(new Class[]
- { FileParse.class });
- final Object[] args = new Object[]
- { new FileParse(getDataName(), type) };
+ final Constructor constructor = cl
+ .getConstructor(new Class[] { FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(),
+ type) };
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
- "getSeqsAsArray", new Class[]
- {}).invoke(jmf));
- cl.getMethod("addAnnotations", new Class[]
- { AlignmentI.class }).invoke(jmf, al);
+ "getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
+ .invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
}
}
- private void replaceAndUpdateChains(List<SequenceI> prot,
- AlignmentI al, String pep, boolean b)
+ private void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+ String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
.replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
{
// TODO: use the PDB ID of the structure if one is available, to save
// bandwidth and avoid uploading the whole structure to the service
- Object annotate3d = cl.getConstructor(new Class[]
- {}).newInstance(new Object[]
- {});
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
+ new Object[] {});
AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
- new Class[]
- { FileParse.class }).invoke(annotate3d, new Object[]
- { new FileParse(getDataName(), type) }));
+ new Class[] { FileParse.class }).invoke(annotate3d,
+ new Object[] { new FileParse(getDataName(), type) }));
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
do
{
i++;
- } while ((i < bonds.size())
- && (bonds.elementAt(i).start[2] < x));
+ } while ((i < bonds.size()) && (bonds.elementAt(i).start[2] < x));
if (i < j)
{
* @author reinert
*/
@Retention(RetentionPolicy.RUNTIME)
-@Target({ElementType.METHOD, ElementType.FIELD, ElementType.TYPE})
-public @interface Attributes {
- String $ref() default "";
+@Target({ ElementType.METHOD, ElementType.FIELD, ElementType.TYPE })
+public @interface Attributes
+{
+ String $ref() default "";
- String id() default "";
+ String id() default "";
- String title() default "";
+ String title() default "";
- String description() default "";
+ String description() default "";
- long maximum() default -1l;
+ long maximum() default -1l;
- boolean exclusiveMaximum() default false;
+ boolean exclusiveMaximum() default false;
- int minimum() default -1;
+ int minimum() default -1;
- boolean exclusiveMinimum() default false;
+ boolean exclusiveMinimum() default false;
- String pattern() default "";
+ String pattern() default "";
- boolean required() default false;
+ boolean required() default false;
- String[] enums() default {};
+ String[] enums() default {};
- int minItems() default 0;
+ int minItems() default 0;
- long maxItems() default -1l;
+ long maxItems() default -1l;
- boolean uniqueItems() default false;
+ boolean uniqueItems() default false;
- int multipleOf() default 0;
+ int multipleOf() default 0;
- int minLength() default 0;
+ int minLength() default 0;
- long maxLength() default -1l;
+ long maxLength() default -1l;
}
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* This is the '.' character in a Pattern. It matches any character.
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** This class represents the \G pattern element. */
class BackG extends Pattern
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* Provides the ability to match a backreference from within a Pattern.
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* Implements the (?<number) Pattern, where number is an integer telling us
* StringWriter(); static PrintWriter pw_s = new PrintWriter(sw,true); public
* static void test(String var,Tester t) throws Exception {
*
- * char[] ca = new char[(66536 >> 4)+1]; Bits b = new Bits(ca); FileWriter fw =
- * new FileWriter("x.out",true); PrintWriter pw = new PrintWriter(fw);
+ * char[] ca = new char[(66536 >> 4)+1]; Bits b = new Bits(ca); FileWriter fw
+ * = new FileWriter("x.out",true); PrintWriter pw = new PrintWriter(fw);
*
* //pw_s.println(" "+var+"_f();"); pw.println(" public static Bits
* "+var+";"); pw.println(" static void "+var+"_f() {"); pw.println(" char[]
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** This class implements the word boundary pattern element: \b. */
class Boundary extends Pattern
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* The Bracket is a form of the Or class, implements the pattern element [ ].
public class Ctrl
{
- public final static char[] cmap =
- { (char) 64, (char) 65, (char) 66, (char) 67, (char) 68, (char) 69,
- (char) 70, (char) 71, (char) 72, (char) 73, (char) 74, (char) 75,
- (char) 76, (char) 77, (char) 78, (char) 79, (char) 80, (char) 81,
- (char) 82, (char) 83, (char) 84, (char) 85, (char) 86, (char) 87,
- (char) 88, (char) 89, (char) 90, (char) 91, (char) 92, (char) 93,
- (char) 94, (char) 95, (char) 96, (char) 97, (char) 97, (char) 99,
- (char) 100, (char) 101, (char) 102, (char) 103, (char) 104,
- (char) 105, (char) 106, (char) 107, (char) 108, (char) 109,
- (char) 110, (char) 111, (char) 112, (char) 113, (char) 114,
- (char) 115, (char) 116, (char) 117, (char) 118, (char) 119,
- (char) 120, (char) 121, (char) 122, (char) 123, (char) 124,
- (char) 125, (char) 126, (char) 127, (char) 0, (char) 1, (char) 2,
- (char) 3, (char) 4, (char) 5, (char) 6, (char) 7, (char) 8, (char) 9,
- (char) 10, (char) 11, (char) 12, (char) 13, (char) 14, (char) 15,
- (char) 16, (char) 17, (char) 18, (char) 19, (char) 20, (char) 21,
- (char) 22, (char) 23, (char) 24, (char) 25, (char) 26, (char) 27,
- (char) 27, (char) 29, (char) 30, (char) 31, (char) 32, (char) 1,
- (char) 2, (char) 3, (char) 4, (char) 5, (char) 6, (char) 7, (char) 8,
- (char) 9, (char) 10, (char) 11, (char) 12, (char) 13, (char) 14,
- (char) 15, (char) 16, (char) 17, (char) 18, (char) 19, (char) 20,
- (char) 21, (char) 22, (char) 23, (char) 24, (char) 25, (char) 26,
- (char) 59, (char) 60, (char) 61, (char) 62, (char) 63, (char) 192,
- (char) 193, (char) 194, (char) 195, (char) 196, (char) 197,
- (char) 198, (char) 199, (char) 200, (char) 201, (char) 202,
- (char) 203, (char) 204, (char) 205, (char) 206, (char) 207,
- (char) 208, (char) 209, (char) 210, (char) 211, (char) 212,
- (char) 213, (char) 214, (char) 215, (char) 216, (char) 217,
- (char) 218, (char) 219, (char) 220, (char) 221, (char) 222,
- (char) 223, (char) 224, (char) 225, (char) 226, (char) 227,
- (char) 228, (char) 229, (char) 230, (char) 231, (char) 232,
- (char) 233, (char) 234, (char) 235, (char) 236, (char) 237,
- (char) 238, (char) 239, (char) 240, (char) 241, (char) 242,
- (char) 243, (char) 244, (char) 245, (char) 246, (char) 247,
- (char) 248, (char) 249, (char) 250, (char) 251, (char) 252,
- (char) 253, (char) 254, (char) 255, (char) 128, (char) 129,
- (char) 130, (char) 131, (char) 132, (char) 133, (char) 134,
- (char) 135, (char) 136, (char) 137, (char) 138, (char) 139,
- (char) 140, (char) 141, (char) 142, (char) 143, (char) 144,
- (char) 145, (char) 146, (char) 147, (char) 148, (char) 149,
- (char) 150, (char) 151, (char) 152, (char) 153, (char) 154,
- (char) 155, (char) 156, (char) 157, (char) 158, (char) 159,
- (char) 160, (char) 161, (char) 162, (char) 163, (char) 164,
- (char) 165, (char) 166, (char) 167, (char) 168, (char) 169,
- (char) 170, (char) 171, (char) 172, (char) 173, (char) 174,
- (char) 175, (char) 176, (char) 177, (char) 178, (char) 179,
- (char) 180, (char) 181, (char) 182, (char) 183, (char) 184,
- (char) 185, (char) 186, (char) 187, (char) 188, (char) 189,
- (char) 190, (char) 191 };
+ public final static char[] cmap = { (char) 64, (char) 65, (char) 66,
+ (char) 67, (char) 68, (char) 69, (char) 70, (char) 71, (char) 72,
+ (char) 73, (char) 74, (char) 75, (char) 76, (char) 77, (char) 78,
+ (char) 79, (char) 80, (char) 81, (char) 82, (char) 83, (char) 84,
+ (char) 85, (char) 86, (char) 87, (char) 88, (char) 89, (char) 90,
+ (char) 91, (char) 92, (char) 93, (char) 94, (char) 95, (char) 96,
+ (char) 97, (char) 97, (char) 99, (char) 100, (char) 101, (char) 102,
+ (char) 103, (char) 104, (char) 105, (char) 106, (char) 107,
+ (char) 108, (char) 109, (char) 110, (char) 111, (char) 112,
+ (char) 113, (char) 114, (char) 115, (char) 116, (char) 117,
+ (char) 118, (char) 119, (char) 120, (char) 121, (char) 122,
+ (char) 123, (char) 124, (char) 125, (char) 126, (char) 127, (char) 0,
+ (char) 1, (char) 2, (char) 3, (char) 4, (char) 5, (char) 6, (char) 7,
+ (char) 8, (char) 9, (char) 10, (char) 11, (char) 12, (char) 13,
+ (char) 14, (char) 15, (char) 16, (char) 17, (char) 18, (char) 19,
+ (char) 20, (char) 21, (char) 22, (char) 23, (char) 24, (char) 25,
+ (char) 26, (char) 27, (char) 27, (char) 29, (char) 30, (char) 31,
+ (char) 32, (char) 1, (char) 2, (char) 3, (char) 4, (char) 5,
+ (char) 6, (char) 7, (char) 8, (char) 9, (char) 10, (char) 11,
+ (char) 12, (char) 13, (char) 14, (char) 15, (char) 16, (char) 17,
+ (char) 18, (char) 19, (char) 20, (char) 21, (char) 22, (char) 23,
+ (char) 24, (char) 25, (char) 26, (char) 59, (char) 60, (char) 61,
+ (char) 62, (char) 63, (char) 192, (char) 193, (char) 194, (char) 195,
+ (char) 196, (char) 197, (char) 198, (char) 199, (char) 200,
+ (char) 201, (char) 202, (char) 203, (char) 204, (char) 205,
+ (char) 206, (char) 207, (char) 208, (char) 209, (char) 210,
+ (char) 211, (char) 212, (char) 213, (char) 214, (char) 215,
+ (char) 216, (char) 217, (char) 218, (char) 219, (char) 220,
+ (char) 221, (char) 222, (char) 223, (char) 224, (char) 225,
+ (char) 226, (char) 227, (char) 228, (char) 229, (char) 230,
+ (char) 231, (char) 232, (char) 233, (char) 234, (char) 235,
+ (char) 236, (char) 237, (char) 238, (char) 239, (char) 240,
+ (char) 241, (char) 242, (char) 243, (char) 244, (char) 245,
+ (char) 246, (char) 247, (char) 248, (char) 249, (char) 250,
+ (char) 251, (char) 252, (char) 253, (char) 254, (char) 255,
+ (char) 128, (char) 129, (char) 130, (char) 131, (char) 132,
+ (char) 133, (char) 134, (char) 135, (char) 136, (char) 137,
+ (char) 138, (char) 139, (char) 140, (char) 141, (char) 142,
+ (char) 143, (char) 144, (char) 145, (char) 146, (char) 147,
+ (char) 148, (char) 149, (char) 150, (char) 151, (char) 152,
+ (char) 153, (char) 154, (char) 155, (char) 156, (char) 157,
+ (char) 158, (char) 159, (char) 160, (char) 161, (char) 162,
+ (char) 163, (char) 164, (char) 165, (char) 166, (char) 167,
+ (char) 168, (char) 169, (char) 170, (char) 171, (char) 172,
+ (char) 173, (char) 174, (char) 175, (char) 176, (char) 177,
+ (char) 178, (char) 179, (char) 180, (char) 181, (char) 182,
+ (char) 183, (char) 184, (char) 185, (char) 186, (char) 187,
+ (char) 188, (char) 189, (char) 190, (char) 191 };
}
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* Simple custom patterns. See <a
* href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> and <a
- * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a> in the
- * test directory.
+ * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a> in the test
+ * directory.
*
* @see com.stevesoft.pat.CustomEndpoint
*/
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* This class is needed internally to make backtracking work correctly in
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* A special optimization of multi that is used when the common subpattern ".*"
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
//class AddToEnd extends RegSyntax {};
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.BitSet;
+import java.util.Vector;
/**
* Uses table lookup to match [] type constructs, but only if it can use a
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* A special case of Multi, implemented when minChars().equals(maxChars()), and
//
package com.stevesoft.pat;
-import java.io.*;
-import java.util.*;
+import java.io.File;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* This class is a different form of Regex designed to work more like the file
* matching utility of a Unix shell. It is implemented by some simple string
- * transformations: <center> <table border=1>
+ * transformations: <center>
+ * <table border=1>
* <tr>
- * <td> FileRegex </td>
- * <td> Regex </td>
+ * <td>FileRegex</td>
+ * <td>Regex</td>
* <tr>
- * <td> * </td>
- * <td> .* </td>
+ * <td>*</td>
+ * <td>.*</td>
* <tr>
- * <td> . </td>
- * <td> \. </td>
+ * <td>.</td>
+ * <td>\.</td>
* <tr>
- * <td> { </td>
- * <td> (?: </td>
+ * <td>{</td>
+ * <td>(?:</td>
* <tr>
- * <td> {?! </td>
- * <td> (?! </td>
+ * <td>{?!</td>
+ * <td>(?!</td>
* <tr>
- * <td> {?= </td>
- * <td> (?= </td>
+ * <td>{?=</td>
+ * <td>(?=</td>
* <tr>
- * <td> {?? </td>
- * <td> (?? </td>
+ * <td>{??</td>
+ * <td>(??</td>
* <tr>
- * <td> } </td>
- * <td> ) </td>
+ * <td></td>
+ * <td>)</td>
* <tr>
- * <td> ? </td>
- * <td> . </td>
+ * <td>?</td>
+ * <td>.</td>
* <tr>
- * <td> {,} </td>
- * <td> (|) </td>
- * </table> </center> Note that a FileRegex pattern always ends with the Regex
- * pattern element "$". If you like to experiment, try making FileRegex's and
- * then printing them out. The toString() method does a decompile of the pattern
- * to a standard Regex. Here are some more complete examples: <center> <table
- * border=3>
+ * <td>{,}</td>
+ * <td>(|)</td>
+ * </table>
+ * </center> Note that a FileRegex pattern always ends with the Regex pattern
+ * element "$". If you like to experiment, try making FileRegex's and then
+ * printing them out. The toString() method does a decompile of the pattern to a
+ * standard Regex. Here are some more complete examples: <center>
+ * <table * border=3>
* <tr>
- * <td> FileRegex </td>
- * <td> Regex </td>
+ * <td>FileRegex</td>
+ * <td>Regex</td>
* <tr>
- * <td>*.java </td>
- * <td> .*\.java$ </td>
+ * <td>*.java</td>
+ * <td>.*\.java$</td>
* <tr>
- * <td>*.{java,html} </td>
- * <td> .*\.(java|html)$ </td>
+ * <td>*.{java,html}</td>
+ * <td>.*\.(java|html)$</td>
* <tr>
- * <td> foo.[chC] </td>
- * <td> foo.[chC]$ </td>
- * </table> </center>
+ * <td>foo.[chC]</td>
+ * <td>foo.[chC]$</td>
+ * </table>
+ * </center>
*/
public class FileRegex extends Regex
{
* Compile a new pattern. Throws
*
* @exception com.stevesoft.pat.RegSyntax
- * for nonsensical patterns like "[9-0]+" just as Regex
- * does.
+ * for nonsensical patterns like "[9-0]+" just as Regex does.
* @see com.stevesoft.pat#compile(java.lang.String)
*/
public void compile(String s) throws RegSyntax
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* This class implements the (?@<>) syntax that matches a balanced parenthesis.
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* Matches any number of instances of sub Pattern this was the hardest method to
/**
* @param a
- * The fewest number of times the sub pattern can match.
+ * The fewest number of times the sub pattern can match.
* @param b
- * The maximum number of times the sub pattern can match.
+ * The maximum number of times the sub pattern can match.
* @param p
- * The sub pattern.
+ * The sub pattern.
* @see Multi_stage2
* @see MultiMin
*/
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* If Multi were not split into a second stage, then a nested Multi would try to
//
com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* The idea behind this class is simply to eliminate the need for testing to see
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* This pattern matches nothing -- it is found in patterns like (hello|world|)
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* This class implements the (?: ... ) extended Pattern. It provides a base
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** Implements the parenthesis pattern subelement. */
class OrMark extends Or
import jalview.util.MessageManager;
-import java.util.*;
+import java.util.Hashtable;
/**
Shareware: package pat
*/
Pattern clone1(Hashtable h)
{
- throw new Error(MessageManager.formatMessage("error.no_such_method_as_clone1_for", new String[]{getClass().getName()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.no_such_method_as_clone1_for", new String[] { getClass()
+ .getName() }));
}
Pattern clone(Hashtable h)
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.BitSet;
/**
* Things that need to be kept track of during a match. Passed along with
/**
* See the example file <a
- * href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for
- * further examples of how this is used. You will probably not want to call it
- * directly.
+ * href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for further
+ * examples of how this is used. You will probably not want to call it directly.
*/
public class PushRule extends SpecialRule
{
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** Thrown when one encounters things like [z-a] */
class BadRangeArgs extends RegSyntax
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/** This class is just like oneChar, but doesn't worry about case. */
class FastChar extends oneChar
for (int i = 0; i < numSubs(); i++)
{
int n = i + 1;
- sb
- .append(" sub(" + n + ")=" + matchedFrom(n) + ":"
- + charsMatched(n));
+ sb.append(" sub(" + n + ")=" + matchedFrom(n) + ":" + charsMatched(n));
}
return sb.toString();
}
import jalview.util.MessageManager;
-import java.io.*;
-import java.util.*;
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.BitSet;
+import java.util.Hashtable;
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
/** Matches a Unicode punctuation character. */
class UnicodePunct extends UniValidator
*
* <pre>
* \d+
- * </pre>, but note that the sequence
+ * </pre>
+ *
+ * , but note that the sequence
*
* <pre>
* (?e=#)
* small differences as well. I will either make my package conform or note them
* as I become aware of them.
* <p>
- * This package supports additional patterns not in perl5: <center> <table
- * border=1>
+ * This package supports additional patterns not in perl5: <center>
+ * <table * border=1>
* <tr>
* <td>(?@())</td>
* <td>Group</td>
* "look behind." It fails if it attempts to move to a position before the
* beginning of the string. "x(?<1)" is equivalent to "(?=x)". The number, 1
* in this example, is the number of characters to move backwards.</td>
- * </table> </center>
- * </dl>
+ * </table>
+ * </center> </dl>
*
* @author Steven R. Brandt
* @version package com.stevesoft.pat, release 1.5.3
* search or matchAt methods.
*
* @exception com.stevesoft.pat.RegSyntax
- * is thrown if a syntax error is encountered in the
- * pattern. For example, "x{3,1}" or "*a" are not valid
- * patterns.
+ * is thrown if a syntax error is encountered in the pattern. For
+ * example, "x{3,1}" or "*a" are not valid patterns.
* @see com.stevesoft.pat.Regex#search
* @see com.stevesoft.pat.Regex#matchAt
*/
{
if (s == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_search"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_given_to_regex_search"));
}
return _search(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_like_given_to_regex_search"));
}
return _search(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_reverse_search"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_given_to_regex_reverse_search"));
}
return _reverseSearch(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_reverse_search"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_like_given_to_regex_reverse_search"));
}
return _reverseSearch(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_region"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.null_string_like_given_to_regex_search_region"));
}
return _search(s, start, end);
}
* if(skipper == null) { for(long i=start;i<=up;i++) { charsMatched_ =
* thePattern.matchAt(s,i,pt); if(charsMatched_ >= 0) { matchFrom_ =
* thePattern.mfrom; marks = pt.marks; gFlagto = matchFrom_+charsMatched_;
- * return didMatch_=true; } } } else { pt.no_check = true; for(long i=start;i<=up;i++) {
- * i = skipper.find(src,i,up); if(i<0) { charsMatched_ = matchFrom_ = -1;
- * return didMatch_ = false; } charsMatched_ = thePattern.matchAt(s,i,pt);
- * if(charsMatched_ >= 0) { matchFrom_ = thePattern.mfrom; marks = pt.marks;
- * gFlagto = matchFrom_+charsMatched_; gFlags = s; return didMatch_=true; }
- * else { i = s.adjustIndex(i); up = s.adjustEnd(i); } } } return
- * didMatch_=false; }
+ * return didMatch_=true; } } } else { pt.no_check = true; for(long
+ * i=start;i<=up;i++) { i = skipper.find(src,i,up); if(i<0) { charsMatched_ =
+ * matchFrom_ = -1; return didMatch_ = false; } charsMatched_ =
+ * thePattern.matchAt(s,i,pt); if(charsMatched_ >= 0) { matchFrom_ =
+ * thePattern.mfrom; marks = pt.marks; gFlagto = matchFrom_+charsMatched_;
+ * gFlags = s; return didMatch_=true; } else { i = s.adjustIndex(i); up =
+ * s.adjustEnd(i); } } } return didMatch_=false; }
*/
boolean _reverseSearch(String s, int start, int end)
* the Pattern.
*
* @exception com.stevesoft.pat.RegSyntax
- * is thrown when a nonsensensical pattern is supplied. For
- * example, a pattern beginning with *.
+ * is thrown when a nonsensensical pattern is supplied. For
+ * example, a pattern beginning with *.
*/
protected void compile1(StrPos sp, Rthings mk) throws RegSyntax
{
* optimized() method.
* <p>
* This method will attempt to rewrite your pattern in a way that makes it
- * faster (not all patterns execute at the same speed). In general, "(?: ... )"
- * will be faster than "( ... )" so if you don't need the backreference, you
- * should group using the former pattern.
+ * faster (not all patterns execute at the same speed). In general,
+ * "(?: ... )" will be faster than "( ... )" so if you don't need the
+ * backreference, you should group using the former pattern.
* <p>
* It will also introduce new pattern elements that you can't get to
* otherwise, for example if you have a large table of strings, i.e. the
//
package com.stevesoft.pat;
-import java.io.*;
+import java.io.IOException;
+import java.io.Reader;
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringBufferWrap;
/**
* This class allows you to replace the text in strings as you read them in. Be
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Enumeration;
+import java.util.Vector;
/**
Shareware: package pat
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* ReplaceRule is a singly linked list of Objects which describe how to replace
import jalview.util.MessageManager;
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
/** Internally used class. */
class RegHolder
lastMatchedTo = 0;
if (rh.me == null)
{
- throw new NullPointerException(MessageManager.getString("exception.replace_null_regex_pointer"));
+ throw new NullPointerException(
+ MessageManager
+ .getString("exception.replace_null_regex_pointer"));
}
if (rh.me._search(s, start, end))
{
else if (p instanceof Or
&& ((Or) p).v.size() == 1
&& !((Or) p).leftForm().equals("(?!")
- && null != (subsk = findSkip((Pattern) ((Or) p).v
- .elementAt(0), ignoreCase, trnc)))
+ && null != (subsk = findSkip(
+ (Pattern) ((Or) p).v.elementAt(0), ignoreCase, trnc)))
{
subsk.offset += offset;
return subsk;
//
package com.stevesoft.pat;
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
/**
* Like Skip, but implements a <a
* href="http://www.dcc.uchile.cl/~rbaeza/handbook/algs/7/713b.srch.p.html">
- * Boyer-Moore-Horspool</a> type search method that has been modified to be
- * more like a "T-search" (see the Michael Tamm''s article in <i>C'T, magazin
- * fuer computer und technic</i>, August 97 p 292). Yet another important
- * source of information for me was the <a
+ * Boyer-Moore-Horspool</a> type search method that has been modified to be more
+ * like a "T-search" (see the Michael Tamm''s article in <i>C'T, magazin fuer
+ * computer und technic</i>, August 97 p 292). Yet another important source of
+ * information for me was the <a
* href="http://www.go2net.com/people/paulp/deep/1997/05/14/"> Deep Magic</a>
* article on string searching. As of this writing, I can beat String's indexOf
* method in many cases.
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/**
* Implements the (?<number) Pattern, where number is an integer telling us
{
// if(pt.no_check || s.regionMatches(pt.ignoreCase,0,pt.src,pos,s.length()))
if (pt.no_check
- || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos, s
- .length()))
+ || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos,
+ s.length()))
{
return nextMatch(pos + s.length(), pt);
}
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** The '^' or the '\A' Pattern, matches the start of a string. */
class Start extends Pattern
* Package pat can search anything that implements this interface. Package pat
* assumes the following:
* <ul>
- * <li>The StringLike object will not change. Calls to charAt(int) will not
- * vary with time.
- * <li>The length of the object being searched is known before the search
- * begins and does not vary with time.
+ * <li>The StringLike object will not change. Calls to charAt(int) will not vary
+ * with time.
+ * <li>The length of the object being searched is known before the search begins
+ * and does not vary with time.
* </ul>
* Note that searching String is probably faster than searching other objects,
* so searching String is still preferred if possible.
import jalview.util.MessageManager;
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
/**
* Replacement rule used by the Transformer.
Regex r = Regex.perlCode(rs);
if (r == null)
{
- throw new NullPointerException(MessageManager.formatMessage("exception.bad_pattern_to_regex_perl_code", new String[]{rs}));
+ throw new NullPointerException(MessageManager.formatMessage(
+ "exception.bad_pattern_to_regex_perl_code",
+ new String[] { rs }));
}
add(r);
}
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** Implements "(?= )" and "(?! )" */
class lookAhead extends Or
//
package com.stevesoft.pat;
-import java.util.*;
+import java.util.Hashtable;
/** This class matches a single character. */
class oneChar extends Pattern
//
com.stevesoft.pat.wrap;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
/**
* Allows the outcome of a replaceAll() or replaceFirst() to be an array of
//
package com.stevesoft.pat.wrap;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
/**
* This provides a wrapper for a char array so that it can be searched by Regex.
import jalview.util.MessageManager;
-import java.io.*;
+import java.io.IOException;
+import java.io.RandomAccessFile;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.Regex;
+import com.stevesoft.pat.StringLike;
/**
* Provides a wrapper for a RandomAccessFile so that it can be searched by
{
}
- throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage("exception.out_of_bounds_for_file", new String[]{
- Integer.valueOf(i).toString(),
- Integer.valueOf(i0).toString(),
- Integer.valueOf(iend).toString()
- }));
+ throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage(
+ "exception.out_of_bounds_for_file", new String[] {
+ Integer.valueOf(i).toString(),
+ Integer.valueOf(i0).toString(),
+ Integer.valueOf(iend).toString() }));
}
public String toString()
//
package com.stevesoft.pat.wrap;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
/**
* This provides a wrapper for StringBuffer to capture the output of a
//
package com.stevesoft.pat.wrap;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
/**
* A basic wrapper for the String object. Regex does not search String directly
//
package com.stevesoft.pat.wrap;
-import java.io.*;
+import java.io.IOException;
+import java.io.Writer;
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
/**
* Allows the outcome of a replaceAll() or replaceFirst() to be directed to a
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
-public abstract class ChimUtils {
-
- private static Logger logger = LoggerFactory
- .getLogger(ChimUtils.class);
-
- static int MAX_SUB_MODELS = 1000;
-
- public static final HashMap<String, String> aaNames;
-
- public static String RESIDUE_ATTR = "ChimeraResidue";
- public static String RINALYZER_ATTR = "RINalyzerResidue";
- public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
-
- /**
- * Parse the model number returned by Chimera and return the int value
- */
- // invoked by the ChimeraModel constructor
- // line = model id #0 type Molecule name 1ert
- public static int[] parseModelNumber(String inputLine) {
- int hash = inputLine.indexOf('#');
- int space = inputLine.indexOf(' ', hash);
- int decimal = inputLine.substring(hash + 1, space).indexOf('.');
- // model number is between hash+1 and space
- int modelNumber = -1;
- int subModelNumber = 0;
- try {
- if (decimal > 0) {
- subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
- space = decimal + hash + 1;
- }
- modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
- } catch (Exception e) {
- logger.warn("Unexpected return from Chimera: " + inputLine, e);
- }
- return new int[] { modelNumber, subModelNumber };
- }
-
- /**
- * Parse the model number returned by Chimera and return the int value
- */
- // invoked by openModel in ChimeraManager
- // line: #1, chain A: hiv-1 protease
- public static int[] parseOpenedModelNumber(String inputLine) {
- int hash = inputLine.indexOf('#');
- int space = inputLine.indexOf(',', hash);
- int decimal = inputLine.substring(hash + 1, space).indexOf('.');
- // model number is between hash+1 and space
- int modelNumber = -1;
- int subModelNumber = 0;
- try {
- if (decimal > 0) {
- subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
- space = decimal + hash + 1;
- }
- modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
- } catch (Exception e) {
- logger.warn("Unexpected return from Chimera: " + inputLine, e);
- }
- return new int[] { modelNumber, subModelNumber };
- }
-
- /**
- * Parse the model identifier returned by Chimera and return the String value
- */
- // invoked by the ChimeraModel constructor
- // line = model id #0 type Molecule name 1ert
- public static String parseModelName(String inputLine) {
- int start = inputLine.indexOf("name ");
- if (start < 0)
- return null;
- // Might get a quoted string (don't understand why, but there you have it)
- if (inputLine.startsWith("\"", start + 5)) {
- start += 6; // Skip over the first quote
- int end = inputLine.lastIndexOf('"');
- if (end >= 1) {
- return inputLine.substring(start, end);
- } else
- return inputLine.substring(start);
- } else {
- return inputLine.substring(start + 5);
- }
- }
-
- public static Color parseModelColor(String inputLine) {
- try {
- int colorStart = inputLine.indexOf("color ");
- String colorString = inputLine.substring(colorStart + 6);
- String[] rgbStrings = colorString.split(",");
- float[] rgbValues = new float[4];
- for (int i = 0; i < rgbStrings.length; i++) {
- Float f = new Float(rgbStrings[i]);
- rgbValues[i] = f.floatValue();
- }
- if (rgbStrings.length == 4) {
- return new Color(rgbValues[0], rgbValues[1], rgbValues[2], rgbValues[3]);
- } else {
- return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
- }
- } catch (Exception ex) {
- logger.warn("Unexpected return from Chimera: " + inputLine, ex);
- }
- return Color.white;
- }
-
- /**
- * Create the key to use for forming the model/submodel key into the modelHash
- *
- * @param model
- * the model number
- * @param subModel
- * the submodel number
- * @return the model key as an Integer
- */
- public static Integer makeModelKey(int model, int subModel) {
- return new Integer(model * MAX_SUB_MODELS + subModel);
- }
-
- // invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraModel getModel(String atomSpec, ChimeraManager chimeraManager) {
- // System.out.println("getting model for "+atomSpec);
- String[] split = atomSpec.split(":");
- // No model specified....
- if (split[0].length() == 0) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
- // System.out.println("model = "+split[0].substring(1));
- int model = 0;
- int submodel = 0;
- try {
- String[] subSplit = split[0].substring(1).split("\\.");
- if (subSplit.length > 0)
- model = Integer.parseInt(subSplit[0]);
- else
- model = Integer.parseInt(split[0].substring(1));
-
- if (subSplit.length > 1)
- submodel = Integer.parseInt(subSplit[1]);
- } catch (Exception e) {
- // ignore
- logger.warn("Unexpected return from Chimera: " + atomSpec, e);
- }
- return chimeraManager.getChimeraModel(model, submodel);
- }
-
- // invoked by the parseConnectivityReplies in CreateStructureNetworkTask
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraResidue getResidue(String atomSpec, ChimeraManager chimeraManager) {
- // System.out.println("Getting residue from: "+atomSpec);
- ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
- if (model == null) {
- model = chimeraManager.getChimeraModel();
- }
- return getResidue(atomSpec, model);
- }
-
- // invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraResidue getResidue(String atomSpec, ChimeraModel model) {
- // System.out.println("Getting residue from: "+atomSpec);
- String[] split = atomSpec.split(":|@");
-
- // Split into residue and chain
- String[] residueChain = split[1].split("\\.");
-
- if (residueChain[0].length() == 0) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
-
- if (residueChain.length == 2 && residueChain[1].length() > 0) {
- ChimeraChain chain = model.getChain(residueChain[1]);
- return chain.getResidue(residueChain[0]);
- }
- return model.getResidue("_", residueChain[0]);
- }
-
- public static ChimeraChain getChain(String atomSpec, ChimeraModel model) {
- String[] split = atomSpec.split(":|@");
-
- // Split into residue and chain
- String[] residueChain = split[1].split("\\.");
- if (residueChain.length == 1) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
- return model.getChain(residueChain[1]);
- }
-
- public static String getAtomName(String atomSpec) {
- String[] split = atomSpec.split("@");
- if (split.length > 1) {
- return split[1];
- }
- return atomSpec;
- }
-
- public static boolean isBackbone(String atom) {
- if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
- || atom.equals("H"))
- return true;
- return false;
- }
-
- public static String getIntSubtype(String node, String atom) {
- String[] split = node.split("#| ");
- String resType = "";
- if (split.length == 2) {
- resType = split[0].trim().toUpperCase();
- } else if (split.length == 3) {
- resType = split[1].trim().toUpperCase();
- }
- if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT")) {
- return "water";
- } else if (aaNames.containsKey(resType)) {
- if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
- || atom.equals("H")) {
- return "mc";
- } else {
- return "sc";
- }
- } else {
- return "other";
- }
- }
-
-
- public static String[] getResKeyParts(String resKey) {
- // [pdbID[.modelNo]#][residueID][.chainID]
- // pdbID := 4-character code | "URL" | "path"
- String[] resKeyParts = new String[4];
- String[] split = resKey.split("#");
- String resChain = null;
- // if no "#" then it is either only a pdb id or a residue or a chain
- if (split.length == 1) {
- // pdb id without model
- if (resKey.length() == 4 && resKey.indexOf("\\.") < 0) {
- parseModelID(resKey, resKeyParts);
- }
- // pdb link or file
- else if (resKey.startsWith("\"")) {
- parseModelID(resKey, resKeyParts);
- }
- // chain and residue or model and number
- else {
- String[] splitSplit = resKey.split("\\.");
- if (splitSplit.length == 1) {
- // only a chain or a residue
- resChain = resKey;
- } else {
- try {
- // pdb with a model
- Integer.parseInt(splitSplit[1]);
- parseModelID(resKey, resKeyParts);
- } catch (NumberFormatException ex) {
- // residue and chain
- resChain = resKey;
- }
- }
- }
- } else if (split.length == 2) {
- // model and residue+chain
- parseModelID(split[0], resKeyParts);
- resChain = split[1];
- } else {
- // model string with "#"
- // TODO: [Optional] Are there more possibilities?
- parseModelID(resKey.substring(0, resKey.lastIndexOf("#")), resKeyParts);
- resChain = resKey.substring(resKey.lastIndexOf("#") + 1, resKey.length());
- }
- if (resChain != null) {
- //System.out.println(resChain);
- String[] resChainSplit = resChain.split("\\.");
- if (resChainSplit.length == 1) {
- // TODO: [Optional] Find a better way to distinguish between chain and residue
- // if only one character and not an int, probably a chain
- if (resChainSplit[0].length() == 1) {
- try {
- Integer.parseInt(resChainSplit[0]);
- resKeyParts[3] = resChainSplit[0];
- } catch (NumberFormatException ex) {
- resKeyParts[2] = resChainSplit[0];
- }
- } else {
- resKeyParts[3] = resChainSplit[0];
- }
- } else if (resChainSplit.length == 2) {
- resKeyParts[2] = resChainSplit[0];
- resKeyParts[3] = resChainSplit[1];
- } else {
- // too many dots?
- logger.info("Could not parse residue identifier: " + resKey);
- }
- }
- // String print = "";
- // for (int i = 0; i < resKeyParts.length; i++) {
- // if (resKeyParts[i] == null) {
- // print += i + ": null\t";
- // } else {
- // print += i + ": " + resKeyParts[i] + ";";
- // }
- // }
- // System.out.println(print);
- return resKeyParts;
- }
-
- public static void parseModelID(String modelID, String[] resKeyParts) {
- if (modelID.startsWith("\"")) {
- if (modelID.endsWith("\"")) {
- resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
- return;
- } else {
- try {
- Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
- modelID.length()));
- resKeyParts[0] = modelID.substring(0, modelID.lastIndexOf("\"") - 1);
- resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
- modelID.length());
- } catch (NumberFormatException ex) {
- resKeyParts[0] = modelID.substring(1);
- }
- }
- } else {
- String[] modelIDNo = modelID.split("\\.");
- if (modelIDNo.length == 1) {
- resKeyParts[0] = modelIDNo[0];
- } else if (modelIDNo.length == 2) {
- try {
- Integer.parseInt(modelIDNo[1]);
- resKeyParts[0] = modelIDNo[0];
- resKeyParts[1] = modelIDNo[1];
- } catch (NumberFormatException ex) {
- resKeyParts[0] = modelID;
- }
- } else {
- logger.info("Could not parse model identifier: " + modelID);
- }
- }
- }
-
- /**
- * This method takes a Cytoscape attribute specification ([structure#][residue][.chainID]) and
- * returns the lowest-level object referenced by the spec. For example, if the spec is "1tkk",
- * this method will return a ChimeraModel. If the spec is ".A", it will return a ChimeraChain,
- * etc.
- *
- * @param attrSpec
- * the specification string
- * @param chimeraManager
- * the Chimera object we're currently using
- * @return a ChimeraStructuralObject of the lowest type
- */
- public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
- ChimeraManager chimeraManager) {
- if (attrSpec == null || attrSpec.indexOf(',') > 0 || attrSpec.indexOf('-') > 0) {
- // No support for either lists or ranges
- logger.warn("No support for identifier: " + attrSpec);
- return null;
- }
-
- String residue = null;
- String model = null;
- String chain = null;
-
- ChimeraModel chimeraModel = null;
- ChimeraChain chimeraChain = null;
- ChimeraResidue chimeraResidue = null;
-
- // System.out.println("Getting object from attribute: "+attrSpec);
- try {
- String[] split = attrSpec.split("#");
- String resChain = null;
- if (split.length == 1) {
- // no model
- resChain = split[0];
- } else if (split.length == 2) {
- // model and rest
- model = split[0];
- resChain = split[1];
- } else {
- // model string with "#"
- model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
- resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1, attrSpec.length());
- }
- if (resChain != null) {
- String[] resChainSplit = resChain.split("\\.");
- if (resChainSplit.length == 1) {
- residue = resChainSplit[0];
- } else if (resChainSplit.length == 2) {
- residue = resChainSplit[0];
- chain = resChainSplit[1];
- } else {
- // too many dots?
- logger.warn("No support for identifier: " + attrSpec);
- }
- }
-
- // if (split.length == 1) {
- // // No model
- // residue = split[0];
- // } else if (split.length == 3) {
- // // We have all three
- // model = split[0];
- // residue = split[1];
- // chain = split[2];
- // } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
- // // Model and Residue
- // model = split[0];
- // residue = split[1];
- // } else {
- // // Residue and Chain
- // residue = split[0];
- // chain = split[1];
- // }
-
- // System.out.println("model = " + model + " chain = " + chain + " residue = " +
- // residue);
- if (model != null) {
- List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
- ModelType.PDB_MODEL);
- if (models.size() == 1) {
- chimeraModel = models.get(0);
- } else {
- try {
- chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(model), 0);
- } catch (NumberFormatException ex) {
- // ignore
- }
- }
- }
- if (chimeraModel == null) {
- chimeraModel = chimeraManager.getChimeraModel();
- }
- // System.out.println("ChimeraModel = " + chimeraModel);
-
- if (chain != null) {
- chimeraChain = chimeraModel.getChain(chain);
- // System.out.println("ChimeraChain = " + chimeraChain);
- }
- if (residue != null) {
- if (chimeraChain != null) {
- chimeraResidue = chimeraChain.getResidue(residue);
- } else {
- chimeraResidue = chimeraModel.getResidue("_", residue);
- }
- // System.out.println("ChimeraResidue = " + chimeraResidue);
- }
-
- if (chimeraResidue != null)
- return chimeraResidue;
-
- if (chimeraChain != null)
- return chimeraChain;
-
- if (chimeraModel != null)
- return chimeraModel;
-
- } catch (Exception ex) {
- logger.warn("Could not parse residue identifier: " + attrSpec, ex);
- }
- return null;
- }
-
- public static ChimeraStructuralObject fromAttribute(String attrSpec,
- ChimeraManager chimeraManager) {
- // TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
- if (attrSpec == null || attrSpec.indexOf(',') > 0) {
- // No support for either lists or ranges
- // System.out.println("No support for identifier: " + attrSpec);
- logger.warn("No support for identifier: " + attrSpec);
- return null;
- }
- String[] modelIDNoResChain = getResKeyParts(attrSpec);
-
- ChimeraModel chimeraModel = null;
- ChimeraChain chimeraChain = null;
- ChimeraResidue chimeraResidue = null;
-
- // System.out.println("Getting object from attribute: "+attrSpec);
- try {
- if (modelIDNoResChain[0] != null) {
- String modelID = modelIDNoResChain[0];
- List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
- ModelType.PDB_MODEL);
- if (models.size() == 1) { // usual case with only one model
- chimeraModel = models.get(0);
- } else if (models.size() > 1 && modelIDNoResChain[1] != null) {
- // there are several submodels
- try {
- int modelNo = Integer.valueOf(modelIDNoResChain[1]);
- for (ChimeraModel model : models) {
- if (model.getSubModelNumber() == modelNo) {
- chimeraModel = model;
- break;
- }
- }
- } catch (NumberFormatException ex) {
- // ignore
- }
- } else {
- // TODO: [Optional] What is this doing?
- try {
- chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(modelID), 0);
- } catch (NumberFormatException ex) {
- // ignore
- }
- }
- }
- if (chimeraModel == null) {
- // TODO: [Optional] Find a better way to handle this case
- // If no model can be matched, continue
- // System.out.println("No matching model could be find for " + attrSpec);
- return null;
- // chimeraModel = chimeraManager.getChimeraModel();
- // logger.warn("No matching model could be find for " + attrSpec + ". Trying with "
- // + chimeraModel.toSpec());
- }
- // System.out.println("ChimeraModel = " + chimeraModel);
-
- if (modelIDNoResChain[3] != null) {
- chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
- // System.out.println("ChimeraChain = " + chimeraChain);
- }
- if (modelIDNoResChain[2] != null) {
- String residue = modelIDNoResChain[2];
- if (chimeraChain != null) {
- chimeraResidue = chimeraChain.getResidue(residue);
- } else if (chimeraModel.getChain("_") != null) {
- chimeraResidue = chimeraModel.getResidue("_", residue);
- } else if (chimeraModel.getChainCount() == 1) {
- chimeraResidue = chimeraModel.getResidue(chimeraModel.getChainNames()
- .iterator().next(), residue);
- }
- // System.out.println("ChimeraResidue = " + chimeraResidue);
- }
-
- if (chimeraResidue != null)
- return chimeraResidue;
-
- if (chimeraChain != null)
- return chimeraChain;
-
- if (chimeraModel != null)
- return chimeraModel;
-
- } catch (Exception ex) {
- // System.out.println("Could not parse chimera identifier: " +
- // attrSpec+"("+ex.getMessage()+")");
- logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
- }
- return null;
- }
-
- /**
- * Search for structure references in the residue list
- *
- * @param residueList
- * the list of residues
- * @return a concatenated list of structures encoded in the list
- */
- public static String findStructures(String residueList) {
- if (residueList == null)
- return null;
- String[] residues = residueList.split(",");
- Map<String, String> structureNameMap = new HashMap<String, String>();
- for (int i = 0; i < residues.length; i++) {
- String[] components = residues[i].split("#");
- if (components.length > 1) {
- structureNameMap.put(components[0], components[1]);
- }
- }
- if (structureNameMap.isEmpty())
- return null;
-
- String structure = null;
- for (String struct : structureNameMap.keySet()) {
- if (structure == null)
- structure = new String();
- else
- structure = structure.concat(",");
- structure = structure.concat(struct);
- }
- return structure;
- }
-
- // invoked by openStructures in StructureManager
- public static List<String> parseFuncRes(List<String> residueNames, String modelName) {
- List<String> resRanges = new ArrayList<String>();
- for (int i = 0; i < residueNames.size(); i++) {
- String residue = residueNames.get(i);
- // Parse out the structure, if there is one
- String[] components = residue.split("#");
- if (components.length > 1 && !modelName.equals(components[0])) {
- continue;
- } else if (components.length > 1) {
- residue = components[1];
- } else if (components.length == 1) {
- residue = components[0];
- }
- // Check to see if we have a range-spec
- String resRange = "";
- if (residue == null || residue.equals("") || residue.length() == 0) {
- continue;
- }
- String[] range = residue.split("-", 2);
- String chain = null;
- for (int res = 0; res < range.length; res++) {
- if (res == 1) {
- resRange = resRange.concat("-");
- if (chain != null && range[res].indexOf('.') == -1)
- range[res] = range[res].concat("." + chain);
- }
-
- if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0) {
- // This is a range spec with the leading residue containing a chain spec
- String[] resChain = range[res].split("\\.");
- chain = resChain[1];
- range[res] = resChain[0];
- }
- // Fix weird SFLD syntax...
- if (range[res].indexOf('|') > 0 && Character.isDigit(range[res].charAt(0))) {
- int offset = range[res].indexOf('|');
- String str = range[res].substring(offset + 1) + range[res].substring(0, offset);
- range[res] = str;
- }
-
- // Convert to legal atom-spec
- if (Character.isDigit(range[res].charAt(0))) {
- resRange = resRange.concat(range[res]);
- } else if (Character.isDigit(range[res].charAt(1))) {
- resRange = resRange.concat(range[res].substring(1));
- } else if (range[res].charAt(0) == '.') {
- // Do we have a chain spec?
- resRange = resRange.concat(range[res]);
- } else {
- resRange = resRange.concat(range[res].substring(3));
- }
- }
- if (!resRanges.contains(resRange)) {
- resRanges.add(resRange);
- }
- }
- return resRanges;
- }
-
- static {
- aaNames = new HashMap<String, String>();
- aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
- aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
- aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
- aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
- aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
- aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
- aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
- aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
- aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
- aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
- aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
- aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
- aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
- aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
- aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
- aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
- aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
- aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
- aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
- aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
- aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
- aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
- aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
- aaNames.put("HOH", "HOH HOH Water [H]O[H]");
- }
-
- /**
- * Convert the amino acid type to a full name
- *
- * @param aaType
- * the residue type to convert
- * @return the full name of the residue
- */
- public static String toFullName(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[2].replace('_', ' ');
- }
-
- /**
- * Convert the amino acid type to a single letter
- *
- * @param aaType
- * the residue type to convert
- * @return the single letter representation of the residue
- */
- public static String toSingleLetter(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[0];
- }
-
- /**
- * Convert the amino acid type to three letters
- *
- * @param aaType
- * the residue type to convert
- * @return the three letter representation of the residue
- */
- public static String toThreeLetter(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[1];
- }
-
- /**
- * Convert the amino acid type to its SMILES string
- *
- * @param aaType
- * the residue type to convert
- * @return the SMILES representation of the residue
- */
- public static String toSMILES(String aaType) {
- if (!aaNames.containsKey(aaType))
- return null;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- if (ids.length < 4)
- return null;
- return ids[3];
- }
-
- public static String getAlignName(ChimeraStructuralObject chimObj) {
- String name = chimObj.getChimeraModel().toString();
- if (chimObj instanceof ChimeraChain) {
- name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
- }
- return name;
- }
+public abstract class ChimUtils
+{
+
+ private static Logger logger = LoggerFactory.getLogger(ChimUtils.class);
+
+ static int MAX_SUB_MODELS = 1000;
+
+ public static final HashMap<String, String> aaNames;
+
+ public static String RESIDUE_ATTR = "ChimeraResidue";
+
+ public static String RINALYZER_ATTR = "RINalyzerResidue";
+
+ public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
+
+ /**
+ * Parse the model number returned by Chimera and return the int value
+ */
+ // invoked by the ChimeraModel constructor
+ // line = model id #0 type Molecule name 1ert
+ public static int[] parseModelNumber(String inputLine)
+ {
+ int hash = inputLine.indexOf('#');
+ int space = inputLine.indexOf(' ', hash);
+ int decimal = inputLine.substring(hash + 1, space).indexOf('.');
+ // model number is between hash+1 and space
+ int modelNumber = -1;
+ int subModelNumber = 0;
+ try
+ {
+ if (decimal > 0)
+ {
+ subModelNumber = Integer.parseInt(inputLine.substring(decimal
+ + hash + 2, space));
+ space = decimal + hash + 1;
+ }
+ modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+ } catch (Exception e)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, e);
+ }
+ return new int[] { modelNumber, subModelNumber };
+ }
+
+ /**
+ * Parse the model number returned by Chimera and return the int value
+ */
+ // invoked by openModel in ChimeraManager
+ // line: #1, chain A: hiv-1 protease
+ public static int[] parseOpenedModelNumber(String inputLine)
+ {
+ int hash = inputLine.indexOf('#');
+ int space = inputLine.indexOf(',', hash);
+ int decimal = inputLine.substring(hash + 1, space).indexOf('.');
+ // model number is between hash+1 and space
+ int modelNumber = -1;
+ int subModelNumber = 0;
+ try
+ {
+ if (decimal > 0)
+ {
+ subModelNumber = Integer.parseInt(inputLine.substring(decimal
+ + hash + 2, space));
+ space = decimal + hash + 1;
+ }
+ modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+ } catch (Exception e)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, e);
+ }
+ return new int[] { modelNumber, subModelNumber };
+ }
+
+ /**
+ * Parse the model identifier returned by Chimera and return the String value
+ */
+ // invoked by the ChimeraModel constructor
+ // line = model id #0 type Molecule name 1ert
+ public static String parseModelName(String inputLine)
+ {
+ int start = inputLine.indexOf("name ");
+ if (start < 0)
+ return null;
+ // Might get a quoted string (don't understand why, but there you have it)
+ if (inputLine.startsWith("\"", start + 5))
+ {
+ start += 6; // Skip over the first quote
+ int end = inputLine.lastIndexOf('"');
+ if (end >= 1)
+ {
+ return inputLine.substring(start, end);
+ }
+ else
+ return inputLine.substring(start);
+ }
+ else
+ {
+ return inputLine.substring(start + 5);
+ }
+ }
+
+ public static Color parseModelColor(String inputLine)
+ {
+ try
+ {
+ int colorStart = inputLine.indexOf("color ");
+ String colorString = inputLine.substring(colorStart + 6);
+ String[] rgbStrings = colorString.split(",");
+ float[] rgbValues = new float[4];
+ for (int i = 0; i < rgbStrings.length; i++)
+ {
+ Float f = new Float(rgbStrings[i]);
+ rgbValues[i] = f.floatValue();
+ }
+ if (rgbStrings.length == 4)
+ {
+ return new Color(rgbValues[0], rgbValues[1], rgbValues[2],
+ rgbValues[3]);
+ }
+ else
+ {
+ return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
+ }
+ } catch (Exception ex)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, ex);
+ }
+ return Color.white;
+ }
+
+ /**
+ * Create the key to use for forming the model/submodel key into the modelHash
+ *
+ * @param model
+ * the model number
+ * @param subModel
+ * the submodel number
+ * @return the model key as an Integer
+ */
+ public static Integer makeModelKey(int model, int subModel)
+ {
+ return new Integer(model * MAX_SUB_MODELS + subModel);
+ }
+
+ // invoked by the getResdiue (parseConnectivityReplies in
+ // CreateStructureNetworkTask)
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraModel getModel(String atomSpec,
+ ChimeraManager chimeraManager)
+ {
+ // System.out.println("getting model for "+atomSpec);
+ String[] split = atomSpec.split(":");
+ // No model specified....
+ if (split[0].length() == 0)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+ // System.out.println("model = "+split[0].substring(1));
+ int model = 0;
+ int submodel = 0;
+ try
+ {
+ String[] subSplit = split[0].substring(1).split("\\.");
+ if (subSplit.length > 0)
+ model = Integer.parseInt(subSplit[0]);
+ else
+ model = Integer.parseInt(split[0].substring(1));
+
+ if (subSplit.length > 1)
+ submodel = Integer.parseInt(subSplit[1]);
+ } catch (Exception e)
+ {
+ // ignore
+ logger.warn("Unexpected return from Chimera: " + atomSpec, e);
+ }
+ return chimeraManager.getChimeraModel(model, submodel);
+ }
+
+ // invoked by the parseConnectivityReplies in CreateStructureNetworkTask
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraResidue getResidue(String atomSpec,
+ ChimeraManager chimeraManager)
+ {
+ // System.out.println("Getting residue from: "+atomSpec);
+ ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
+ if (model == null)
+ {
+ model = chimeraManager.getChimeraModel();
+ }
+ return getResidue(atomSpec, model);
+ }
+
+ // invoked by the getResdiue (parseConnectivityReplies in
+ // CreateStructureNetworkTask)
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraResidue getResidue(String atomSpec,
+ ChimeraModel model)
+ {
+ // System.out.println("Getting residue from: "+atomSpec);
+ String[] split = atomSpec.split(":|@");
+
+ // Split into residue and chain
+ String[] residueChain = split[1].split("\\.");
+
+ if (residueChain[0].length() == 0)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+
+ if (residueChain.length == 2 && residueChain[1].length() > 0)
+ {
+ ChimeraChain chain = model.getChain(residueChain[1]);
+ return chain.getResidue(residueChain[0]);
+ }
+ return model.getResidue("_", residueChain[0]);
+ }
+
+ public static ChimeraChain getChain(String atomSpec, ChimeraModel model)
+ {
+ String[] split = atomSpec.split(":|@");
+
+ // Split into residue and chain
+ String[] residueChain = split[1].split("\\.");
+ if (residueChain.length == 1)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+ return model.getChain(residueChain[1]);
+ }
+
+ public static String getAtomName(String atomSpec)
+ {
+ String[] split = atomSpec.split("@");
+ if (split.length > 1)
+ {
+ return split[1];
+ }
+ return atomSpec;
+ }
+
+ public static boolean isBackbone(String atom)
+ {
+ if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+ || atom.equals("O") || atom.equals("H"))
+ return true;
+ return false;
+ }
+
+ public static String getIntSubtype(String node, String atom)
+ {
+ String[] split = node.split("#| ");
+ String resType = "";
+ if (split.length == 2)
+ {
+ resType = split[0].trim().toUpperCase();
+ }
+ else if (split.length == 3)
+ {
+ resType = split[1].trim().toUpperCase();
+ }
+ if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
+ {
+ return "water";
+ }
+ else if (aaNames.containsKey(resType))
+ {
+ if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+ || atom.equals("O") || atom.equals("H"))
+ {
+ return "mc";
+ }
+ else
+ {
+ return "sc";
+ }
+ }
+ else
+ {
+ return "other";
+ }
+ }
+
+ public static String[] getResKeyParts(String resKey)
+ {
+ // [pdbID[.modelNo]#][residueID][.chainID]
+ // pdbID := 4-character code | "URL" | "path"
+ String[] resKeyParts = new String[4];
+ String[] split = resKey.split("#");
+ String resChain = null;
+ // if no "#" then it is either only a pdb id or a residue or a chain
+ if (split.length == 1)
+ {
+ // pdb id without model
+ if (resKey.length() == 4 && resKey.indexOf("\\.") < 0)
+ {
+ parseModelID(resKey, resKeyParts);
+ }
+ // pdb link or file
+ else if (resKey.startsWith("\""))
+ {
+ parseModelID(resKey, resKeyParts);
+ }
+ // chain and residue or model and number
+ else
+ {
+ String[] splitSplit = resKey.split("\\.");
+ if (splitSplit.length == 1)
+ {
+ // only a chain or a residue
+ resChain = resKey;
+ }
+ else
+ {
+ try
+ {
+ // pdb with a model
+ Integer.parseInt(splitSplit[1]);
+ parseModelID(resKey, resKeyParts);
+ } catch (NumberFormatException ex)
+ {
+ // residue and chain
+ resChain = resKey;
+ }
+ }
+ }
+ }
+ else if (split.length == 2)
+ {
+ // model and residue+chain
+ parseModelID(split[0], resKeyParts);
+ resChain = split[1];
+ }
+ else
+ {
+ // model string with "#"
+ // TODO: [Optional] Are there more possibilities?
+ parseModelID(resKey.substring(0, resKey.lastIndexOf("#")),
+ resKeyParts);
+ resChain = resKey.substring(resKey.lastIndexOf("#") + 1,
+ resKey.length());
+ }
+ if (resChain != null)
+ {
+ // System.out.println(resChain);
+ String[] resChainSplit = resChain.split("\\.");
+ if (resChainSplit.length == 1)
+ {
+ // TODO: [Optional] Find a better way to distinguish between chain and
+ // residue
+ // if only one character and not an int, probably a chain
+ if (resChainSplit[0].length() == 1)
+ {
+ try
+ {
+ Integer.parseInt(resChainSplit[0]);
+ resKeyParts[3] = resChainSplit[0];
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[2] = resChainSplit[0];
+ }
+ }
+ else
+ {
+ resKeyParts[3] = resChainSplit[0];
+ }
+ }
+ else if (resChainSplit.length == 2)
+ {
+ resKeyParts[2] = resChainSplit[0];
+ resKeyParts[3] = resChainSplit[1];
+ }
+ else
+ {
+ // too many dots?
+ logger.info("Could not parse residue identifier: " + resKey);
+ }
+ }
+ // String print = "";
+ // for (int i = 0; i < resKeyParts.length; i++) {
+ // if (resKeyParts[i] == null) {
+ // print += i + ": null\t";
+ // } else {
+ // print += i + ": " + resKeyParts[i] + ";";
+ // }
+ // }
+ // System.out.println(print);
+ return resKeyParts;
+ }
+
+ public static void parseModelID(String modelID, String[] resKeyParts)
+ {
+ if (modelID.startsWith("\""))
+ {
+ if (modelID.endsWith("\""))
+ {
+ resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
+ return;
+ }
+ else
+ {
+ try
+ {
+ Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
+ modelID.length()));
+ resKeyParts[0] = modelID.substring(0,
+ modelID.lastIndexOf("\"") - 1);
+ resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
+ modelID.length());
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[0] = modelID.substring(1);
+ }
+ }
+ }
+ else
+ {
+ String[] modelIDNo = modelID.split("\\.");
+ if (modelIDNo.length == 1)
+ {
+ resKeyParts[0] = modelIDNo[0];
+ }
+ else if (modelIDNo.length == 2)
+ {
+ try
+ {
+ Integer.parseInt(modelIDNo[1]);
+ resKeyParts[0] = modelIDNo[0];
+ resKeyParts[1] = modelIDNo[1];
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[0] = modelID;
+ }
+ }
+ else
+ {
+ logger.info("Could not parse model identifier: " + modelID);
+ }
+ }
+ }
+
+ /**
+ * This method takes a Cytoscape attribute specification
+ * ([structure#][residue][.chainID]) and returns the lowest-level object
+ * referenced by the spec. For example, if the spec is "1tkk", this method
+ * will return a ChimeraModel. If the spec is ".A", it will return a
+ * ChimeraChain, etc.
+ *
+ * @param attrSpec
+ * the specification string
+ * @param chimeraManager
+ * the Chimera object we're currently using
+ * @return a ChimeraStructuralObject of the lowest type
+ */
+ public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
+ ChimeraManager chimeraManager)
+ {
+ if (attrSpec == null || attrSpec.indexOf(',') > 0
+ || attrSpec.indexOf('-') > 0)
+ {
+ // No support for either lists or ranges
+ logger.warn("No support for identifier: " + attrSpec);
+ return null;
+ }
+
+ String residue = null;
+ String model = null;
+ String chain = null;
+
+ ChimeraModel chimeraModel = null;
+ ChimeraChain chimeraChain = null;
+ ChimeraResidue chimeraResidue = null;
+
+ // System.out.println("Getting object from attribute: "+attrSpec);
+ try
+ {
+ String[] split = attrSpec.split("#");
+ String resChain = null;
+ if (split.length == 1)
+ {
+ // no model
+ resChain = split[0];
+ }
+ else if (split.length == 2)
+ {
+ // model and rest
+ model = split[0];
+ resChain = split[1];
+ }
+ else
+ {
+ // model string with "#"
+ model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
+ resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1,
+ attrSpec.length());
+ }
+ if (resChain != null)
+ {
+ String[] resChainSplit = resChain.split("\\.");
+ if (resChainSplit.length == 1)
+ {
+ residue = resChainSplit[0];
+ }
+ else if (resChainSplit.length == 2)
+ {
+ residue = resChainSplit[0];
+ chain = resChainSplit[1];
+ }
+ else
+ {
+ // too many dots?
+ logger.warn("No support for identifier: " + attrSpec);
+ }
+ }
+
+ // if (split.length == 1) {
+ // // No model
+ // residue = split[0];
+ // } else if (split.length == 3) {
+ // // We have all three
+ // model = split[0];
+ // residue = split[1];
+ // chain = split[2];
+ // } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
+ // // Model and Residue
+ // model = split[0];
+ // residue = split[1];
+ // } else {
+ // // Residue and Chain
+ // residue = split[0];
+ // chain = split[1];
+ // }
+
+ // System.out.println("model = " + model + " chain = " + chain +
+ // " residue = " +
+ // residue);
+ if (model != null)
+ {
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
+ ModelType.PDB_MODEL);
+ if (models.size() == 1)
+ {
+ chimeraModel = models.get(0);
+ }
+ else
+ {
+ try
+ {
+ chimeraModel = chimeraManager.getChimeraModel(
+ Integer.valueOf(model), 0);
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ }
+ if (chimeraModel == null)
+ {
+ chimeraModel = chimeraManager.getChimeraModel();
+ }
+ // System.out.println("ChimeraModel = " + chimeraModel);
+
+ if (chain != null)
+ {
+ chimeraChain = chimeraModel.getChain(chain);
+ // System.out.println("ChimeraChain = " + chimeraChain);
+ }
+ if (residue != null)
+ {
+ if (chimeraChain != null)
+ {
+ chimeraResidue = chimeraChain.getResidue(residue);
+ }
+ else
+ {
+ chimeraResidue = chimeraModel.getResidue("_", residue);
+ }
+ // System.out.println("ChimeraResidue = " + chimeraResidue);
+ }
+
+ if (chimeraResidue != null)
+ return chimeraResidue;
+
+ if (chimeraChain != null)
+ return chimeraChain;
+
+ if (chimeraModel != null)
+ return chimeraModel;
+
+ } catch (Exception ex)
+ {
+ logger.warn("Could not parse residue identifier: " + attrSpec, ex);
+ }
+ return null;
+ }
+
+ public static ChimeraStructuralObject fromAttribute(String attrSpec,
+ ChimeraManager chimeraManager)
+ {
+ // TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
+ if (attrSpec == null || attrSpec.indexOf(',') > 0)
+ {
+ // No support for either lists or ranges
+ // System.out.println("No support for identifier: " + attrSpec);
+ logger.warn("No support for identifier: " + attrSpec);
+ return null;
+ }
+ String[] modelIDNoResChain = getResKeyParts(attrSpec);
+
+ ChimeraModel chimeraModel = null;
+ ChimeraChain chimeraChain = null;
+ ChimeraResidue chimeraResidue = null;
+
+ // System.out.println("Getting object from attribute: "+attrSpec);
+ try
+ {
+ if (modelIDNoResChain[0] != null)
+ {
+ String modelID = modelIDNoResChain[0];
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(
+ modelID, ModelType.PDB_MODEL);
+ if (models.size() == 1)
+ { // usual case with only one model
+ chimeraModel = models.get(0);
+ }
+ else if (models.size() > 1 && modelIDNoResChain[1] != null)
+ {
+ // there are several submodels
+ try
+ {
+ int modelNo = Integer.valueOf(modelIDNoResChain[1]);
+ for (ChimeraModel model : models)
+ {
+ if (model.getSubModelNumber() == modelNo)
+ {
+ chimeraModel = model;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ else
+ {
+ // TODO: [Optional] What is this doing?
+ try
+ {
+ chimeraModel = chimeraManager.getChimeraModel(
+ Integer.valueOf(modelID), 0);
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ }
+ if (chimeraModel == null)
+ {
+ // TODO: [Optional] Find a better way to handle this case
+ // If no model can be matched, continue
+ // System.out.println("No matching model could be find for " +
+ // attrSpec);
+ return null;
+ // chimeraModel = chimeraManager.getChimeraModel();
+ // logger.warn("No matching model could be find for " + attrSpec +
+ // ". Trying with "
+ // + chimeraModel.toSpec());
+ }
+ // System.out.println("ChimeraModel = " + chimeraModel);
+
+ if (modelIDNoResChain[3] != null)
+ {
+ chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
+ // System.out.println("ChimeraChain = " + chimeraChain);
+ }
+ if (modelIDNoResChain[2] != null)
+ {
+ String residue = modelIDNoResChain[2];
+ if (chimeraChain != null)
+ {
+ chimeraResidue = chimeraChain.getResidue(residue);
+ }
+ else if (chimeraModel.getChain("_") != null)
+ {
+ chimeraResidue = chimeraModel.getResidue("_", residue);
+ }
+ else if (chimeraModel.getChainCount() == 1)
+ {
+ chimeraResidue = chimeraModel.getResidue(chimeraModel
+ .getChainNames().iterator().next(), residue);
+ }
+ // System.out.println("ChimeraResidue = " + chimeraResidue);
+ }
+
+ if (chimeraResidue != null)
+ return chimeraResidue;
+
+ if (chimeraChain != null)
+ return chimeraChain;
+
+ if (chimeraModel != null)
+ return chimeraModel;
+
+ } catch (Exception ex)
+ {
+ // System.out.println("Could not parse chimera identifier: " +
+ // attrSpec+"("+ex.getMessage()+")");
+ logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
+ }
+ return null;
+ }
+
+ /**
+ * Search for structure references in the residue list
+ *
+ * @param residueList
+ * the list of residues
+ * @return a concatenated list of structures encoded in the list
+ */
+ public static String findStructures(String residueList)
+ {
+ if (residueList == null)
+ return null;
+ String[] residues = residueList.split(",");
+ Map<String, String> structureNameMap = new HashMap<String, String>();
+ for (int i = 0; i < residues.length; i++)
+ {
+ String[] components = residues[i].split("#");
+ if (components.length > 1)
+ {
+ structureNameMap.put(components[0], components[1]);
+ }
+ }
+ if (structureNameMap.isEmpty())
+ return null;
+
+ String structure = null;
+ for (String struct : structureNameMap.keySet())
+ {
+ if (structure == null)
+ structure = new String();
+ else
+ structure = structure.concat(",");
+ structure = structure.concat(struct);
+ }
+ return structure;
+ }
+
+ // invoked by openStructures in StructureManager
+ public static List<String> parseFuncRes(List<String> residueNames,
+ String modelName)
+ {
+ List<String> resRanges = new ArrayList<String>();
+ for (int i = 0; i < residueNames.size(); i++)
+ {
+ String residue = residueNames.get(i);
+ // Parse out the structure, if there is one
+ String[] components = residue.split("#");
+ if (components.length > 1 && !modelName.equals(components[0]))
+ {
+ continue;
+ }
+ else if (components.length > 1)
+ {
+ residue = components[1];
+ }
+ else if (components.length == 1)
+ {
+ residue = components[0];
+ }
+ // Check to see if we have a range-spec
+ String resRange = "";
+ if (residue == null || residue.equals("") || residue.length() == 0)
+ {
+ continue;
+ }
+ String[] range = residue.split("-", 2);
+ String chain = null;
+ for (int res = 0; res < range.length; res++)
+ {
+ if (res == 1)
+ {
+ resRange = resRange.concat("-");
+ if (chain != null && range[res].indexOf('.') == -1)
+ range[res] = range[res].concat("." + chain);
+ }
+
+ if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0)
+ {
+ // This is a range spec with the leading residue containing a chain
+ // spec
+ String[] resChain = range[res].split("\\.");
+ chain = resChain[1];
+ range[res] = resChain[0];
+ }
+ // Fix weird SFLD syntax...
+ if (range[res].indexOf('|') > 0
+ && Character.isDigit(range[res].charAt(0)))
+ {
+ int offset = range[res].indexOf('|');
+ String str = range[res].substring(offset + 1)
+ + range[res].substring(0, offset);
+ range[res] = str;
+ }
+
+ // Convert to legal atom-spec
+ if (Character.isDigit(range[res].charAt(0)))
+ {
+ resRange = resRange.concat(range[res]);
+ }
+ else if (Character.isDigit(range[res].charAt(1)))
+ {
+ resRange = resRange.concat(range[res].substring(1));
+ }
+ else if (range[res].charAt(0) == '.')
+ {
+ // Do we have a chain spec?
+ resRange = resRange.concat(range[res]);
+ }
+ else
+ {
+ resRange = resRange.concat(range[res].substring(3));
+ }
+ }
+ if (!resRanges.contains(resRange))
+ {
+ resRanges.add(resRange);
+ }
+ }
+ return resRanges;
+ }
+
+ static
+ {
+ aaNames = new HashMap<String, String>();
+ aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+ aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+ aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+ aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+ aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+ aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+ aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+ aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+ aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+ aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+ aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+ aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+ aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+ aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+ aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+ aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+ aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+ aaNames.put("TRP",
+ "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+ aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+ aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+ aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+ aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+ aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+ aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+ }
+
+ /**
+ * Convert the amino acid type to a full name
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the full name of the residue
+ */
+ public static String toFullName(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ return aaType;
+ String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ return ids[2].replace('_', ' ');
+ }
+
+ /**
+ * Convert the amino acid type to a single letter
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the single letter representation of the residue
+ */
+ public static String toSingleLetter(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ return aaType;
+ String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ return ids[0];
+ }
+
+ /**
+ * Convert the amino acid type to three letters
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the three letter representation of the residue
+ */
+ public static String toThreeLetter(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ return aaType;
+ String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ return ids[1];
+ }
+
+ /**
+ * Convert the amino acid type to its SMILES string
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the SMILES representation of the residue
+ */
+ public static String toSMILES(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ return null;
+ String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ if (ids.length < 4)
+ return null;
+ return ids[3];
+ }
+
+ public static String getAlignName(ChimeraStructuralObject chimObj)
+ {
+ String name = chimObj.getChimeraModel().toString();
+ if (chimObj instanceof ChimeraChain)
+ {
+ name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
+ }
+ return name;
+ }
}
*
*/
// TODO: [Optional] Implement toAttr() method
-public class ChimeraChain implements ChimeraStructuralObject {
+public class ChimeraChain implements ChimeraStructuralObject
+{
- /**
- * The model/subModel number this chain is a part of
- */
- private int modelNumber;
- private int subModelNumber;
+ /**
+ * The model/subModel number this chain is a part of
+ */
+ private int modelNumber;
- /**
- * A pointer to the model this chain is a part of
- */
- private ChimeraModel chimeraModel;
+ private int subModelNumber;
- /**
- * The chainID (from the PDB record)
- */
- private String chainId;
+ /**
+ * A pointer to the model this chain is a part of
+ */
+ private ChimeraModel chimeraModel;
- /**
- * The residues that are part of this chain
- */
- private TreeMap<String, ChimeraResidue> residueMap;
+ /**
+ * The chainID (from the PDB record)
+ */
+ private String chainId;
- /**
- * userData to associate with this chain
- */
- private Object userData;
+ /**
+ * The residues that are part of this chain
+ */
+ private TreeMap<String, ChimeraResidue> residueMap;
- /**
- * Flag to indicate the selection state
- */
- private boolean selected = false;
+ /**
+ * userData to associate with this chain
+ */
+ private Object userData;
- /**
- * Constructor to create a new ChimeraChain
- *
- * @param model
- * the model number this chain is part of
- * @param subModel
- * the subModel number this chain is part of
- * @param chainId
- * the chain ID for this chain
- */
- public ChimeraChain(int model, int subModel, String chainId) {
- this.modelNumber = model;
- this.subModelNumber = subModel;
- this.chainId = chainId;
- residueMap = new TreeMap<String, ChimeraResidue>();
- }
+ /**
+ * Flag to indicate the selection state
+ */
+ private boolean selected = false;
- /**
- * set the selected state of this chain
- *
- * @param selected
- * a boolean to set the selected state to
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
+ /**
+ * Constructor to create a new ChimeraChain
+ *
+ * @param model
+ * the model number this chain is part of
+ * @param subModel
+ * the subModel number this chain is part of
+ * @param chainId
+ * the chain ID for this chain
+ */
+ public ChimeraChain(int model, int subModel, String chainId)
+ {
+ this.modelNumber = model;
+ this.subModelNumber = subModel;
+ this.chainId = chainId;
+ residueMap = new TreeMap<String, ChimeraResidue>();
+ }
- /**
- * return the selected state of this chain
- *
- * @return the selected state
- */
- public boolean isSelected() {
- return selected;
- }
+ /**
+ * set the selected state of this chain
+ *
+ * @param selected
+ * a boolean to set the selected state to
+ */
+ public void setSelected(boolean selected)
+ {
+ this.selected = selected;
+ }
- public boolean hasSelectedChildren() {
- if (selected) {
- return true;
- } else {
- for (ChimeraResidue residue : getResidues()) {
- if (residue.isSelected())
- return true;
- }
- }
- return false;
- }
+ /**
+ * return the selected state of this chain
+ *
+ * @return the selected state
+ */
+ public boolean isSelected()
+ {
+ return selected;
+ }
- /**
- * Return the list of selected residues
- *
- * @return all selected residues
- */
- public List<ChimeraResidue> getSelectedResidues() {
- List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
- if (selected) {
- residueList.addAll(getResidues());
- } else {
- for (ChimeraResidue residue : getResidues()) {
- if (residue.isSelected())
- residueList.add(residue);
- }
- }
- return residueList;
- }
+ public boolean hasSelectedChildren()
+ {
+ if (selected)
+ {
+ return true;
+ }
+ else
+ {
+ for (ChimeraResidue residue : getResidues())
+ {
+ if (residue.isSelected())
+ return true;
+ }
+ }
+ return false;
+ }
- /**
- * Add a residue to the chain.
- *
- * @param residue
- * the ChimeraResidue to add to the chain.
- */
- public void addResidue(ChimeraResidue residue) {
- String index = residue.getIndex();
- // Put it in our map so that we can return it in order
- residueMap.put(index, residue);
- }
+ /**
+ * Return the list of selected residues
+ *
+ * @return all selected residues
+ */
+ public List<ChimeraResidue> getSelectedResidues()
+ {
+ List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
+ if (selected)
+ {
+ residueList.addAll(getResidues());
+ }
+ else
+ {
+ for (ChimeraResidue residue : getResidues())
+ {
+ if (residue.isSelected())
+ residueList.add(residue);
+ }
+ }
+ return residueList;
+ }
- /**
- * Return the list of residues in this chain in pdb residue order
- *
- * @return a Collection of residues in residue order
- */
- public Collection<ChimeraResidue> getResidues() {
- return residueMap.values();
- }
+ /**
+ * Add a residue to the chain.
+ *
+ * @param residue
+ * the ChimeraResidue to add to the chain.
+ */
+ public void addResidue(ChimeraResidue residue)
+ {
+ String index = residue.getIndex();
+ // Put it in our map so that we can return it in order
+ residueMap.put(index, residue);
+ }
- /**
- * Return the list of residues in this chain as a list
- *
- * @return List of residues
- */
- public List<ChimeraStructuralObject> getChildren() {
- return new ArrayList<ChimeraStructuralObject>(residueMap.values());
- }
+ /**
+ * Return the list of residues in this chain in pdb residue order
+ *
+ * @return a Collection of residues in residue order
+ */
+ public Collection<ChimeraResidue> getResidues()
+ {
+ return residueMap.values();
+ }
- /**
- * Get a specific residue
- *
- * @param residueIndex
- * String representation of the residue index
- * @return the ChimeraResidue represented by the residueIndex
- */
- public ChimeraResidue getResidue(String index) {
- // Integer index = new Integer(residueIndex);
- if (residueMap.containsKey(index))
- return residueMap.get(index);
- return null;
- }
+ /**
+ * Return the list of residues in this chain as a list
+ *
+ * @return List of residues
+ */
+ public List<ChimeraStructuralObject> getChildren()
+ {
+ return new ArrayList<ChimeraStructuralObject>(residueMap.values());
+ }
- /**
- * Get a list of residues as a residue range
- *
- * @param residueRange
- * String representation of the residue range
- * @return the List of ChimeraResidues represented by the range
- */
- public List<ChimeraResidue> getResidueRange(String residueRange) {
- String[] range = residueRange.split("-", 2);
- if (range[1] == null || range[1].length() == 0) {
- range[1] = range[0];
- }
- List<ChimeraResidue> resultRange = new ArrayList<ChimeraResidue>();
- int start = Integer.parseInt(range[0]);
- int end = Integer.parseInt(range[1]);
- for (int i = start; i <= end; i++) {
- String index = String.valueOf(i);
- if (residueMap.containsKey(index))
- resultRange.add(residueMap.get(index));
- }
- return resultRange;
- }
+ /**
+ * Get a specific residue
+ *
+ * @param residueIndex
+ * String representation of the residue index
+ * @return the ChimeraResidue represented by the residueIndex
+ */
+ public ChimeraResidue getResidue(String index)
+ {
+ // Integer index = new Integer(residueIndex);
+ if (residueMap.containsKey(index))
+ return residueMap.get(index);
+ return null;
+ }
- /**
- * Get the ID for this chain
- *
- * @return String value of the chainId
- */
- public String getChainId() {
- return chainId;
- }
+ /**
+ * Get a list of residues as a residue range
+ *
+ * @param residueRange
+ * String representation of the residue range
+ * @return the List of ChimeraResidues represented by the range
+ */
+ public List<ChimeraResidue> getResidueRange(String residueRange)
+ {
+ String[] range = residueRange.split("-", 2);
+ if (range[1] == null || range[1].length() == 0)
+ {
+ range[1] = range[0];
+ }
+ List<ChimeraResidue> resultRange = new ArrayList<ChimeraResidue>();
+ int start = Integer.parseInt(range[0]);
+ int end = Integer.parseInt(range[1]);
+ for (int i = start; i <= end; i++)
+ {
+ String index = String.valueOf(i);
+ if (residueMap.containsKey(index))
+ resultRange.add(residueMap.get(index));
+ }
+ return resultRange;
+ }
- /**
- * Get the model number for this chain
- *
- * @return the model number
- */
- public int getModelNumber() {
- return modelNumber;
- }
+ /**
+ * Get the ID for this chain
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId()
+ {
+ return chainId;
+ }
- /**
- * Get the sub-model number for this chain
- *
- * @return the sub-model number
- */
- public int getSubModelNumber() {
- return subModelNumber;
- }
+ /**
+ * Get the model number for this chain
+ *
+ * @return the model number
+ */
+ public int getModelNumber()
+ {
+ return modelNumber;
+ }
- /**
- * Return a string representation of this chain as follows: Chain <i>chainId</i>
- * (<i>residue_count</i> residues)
- *
- * @return String representation of chain
- */
- public String displayName() {
- if (chainId.equals("_")) {
- return ("Chain (no ID) (" + getResidueCount() + " residues)");
- } else {
- return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
- }
- }
+ /**
+ * Get the sub-model number for this chain
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber()
+ {
+ return subModelNumber;
+ }
- /**
- * Return a string representation of this chain as follows: Node xxx [Model yyyy Chain
- * <i>chainId</i>]
- *
- * @return String representation of chain
- */
- public String toString() {
- String displayName = chimeraModel.getModelName();
- if (displayName.length() > 14)
- displayName = displayName.substring(0, 13) + "...";
- if (chainId.equals("_")) {
- return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
- } else {
- return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
- }
- }
+ /**
+ * Return a string representation of this chain as follows: Chain
+ * <i>chainId</i> (<i>residue_count</i> residues)
+ *
+ * @return String representation of chain
+ */
+ public String displayName()
+ {
+ if (chainId.equals("_"))
+ {
+ return ("Chain (no ID) (" + getResidueCount() + " residues)");
+ }
+ else
+ {
+ return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
+ }
+ }
- /**
- * Return the Chimera specification for this chain
- *
- * @return Chimera specification
- */
- public String toSpec() {
- if (chainId.equals("_")) {
- return ("#" + modelNumber + "." + subModelNumber + ":.");
- } else {
- return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
- }
- }
+ /**
+ * Return a string representation of this chain as follows: Node xxx [Model
+ * yyyy Chain <i>chainId</i>]
+ *
+ * @return String representation of chain
+ */
+ public String toString()
+ {
+ String displayName = chimeraModel.getModelName();
+ if (displayName.length() > 14)
+ displayName = displayName.substring(0, 13) + "...";
+ if (chainId.equals("_"))
+ {
+ return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
+ }
+ else
+ {
+ return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
+ }
+ }
- /**
- * Return the number of residues in this chain
- *
- * @return integer number of residues
- */
- public int getResidueCount() {
- return residueMap.size();
- }
+ /**
+ * Return the Chimera specification for this chain
+ *
+ * @return Chimera specification
+ */
+ public String toSpec()
+ {
+ if (chainId.equals("_"))
+ {
+ return ("#" + modelNumber + "." + subModelNumber + ":.");
+ }
+ else
+ {
+ return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
+ }
+ }
- /**
- * Set the ChimeraModel for this chain
- *
- * @param model
- * ChimeraModel to associate with this chain
- */
- public void setChimeraModel(ChimeraModel model) {
- this.chimeraModel = model;
- }
+ /**
+ * Return the number of residues in this chain
+ *
+ * @return integer number of residues
+ */
+ public int getResidueCount()
+ {
+ return residueMap.size();
+ }
- /**
- * Get the ChimeraModel for this chain
- *
- * @return ChimeraModel associated with this chain
- */
- public ChimeraModel getChimeraModel() {
- return chimeraModel;
- }
+ /**
+ * Set the ChimeraModel for this chain
+ *
+ * @param model
+ * ChimeraModel to associate with this chain
+ */
+ public void setChimeraModel(ChimeraModel model)
+ {
+ this.chimeraModel = model;
+ }
- /**
- * Get the user data for this Chain
- *
- * @return user data
- */
- public Object getUserData() {
- return userData;
- }
+ /**
+ * Get the ChimeraModel for this chain
+ *
+ * @return ChimeraModel associated with this chain
+ */
+ public ChimeraModel getChimeraModel()
+ {
+ return chimeraModel;
+ }
- /**
- * Set the user data for this Chain
- *
- * @param data
- * the user data to associate with this chain
- */
- public void setUserData(Object data) {
- this.userData = data;
- }
+ /**
+ * Get the user data for this Chain
+ *
+ * @return user data
+ */
+ public Object getUserData()
+ {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this Chain
+ *
+ * @param data
+ * the user data to associate with this chain
+ */
+ public void setUserData(Object data)
+ {
+ this.userData = data;
+ }
}
// TODO: [Optional] Convert path to name in a better way
if (modelPath.lastIndexOf(File.separator) > 0)
{
- modelName = modelPath.substring(modelPath
- .lastIndexOf(File.separator) + 1);
+ modelName = modelPath
+ .substring(modelPath.lastIndexOf(File.separator) + 1);
}
else if (modelPath.lastIndexOf("/") > 0)
{
- modelName = modelPath
- .substring(modelPath.lastIndexOf("/") + 1);
+ modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
}
return modelName;
}
public void startListening(String uri)
{
sendChimeraCommand("listen start models url " + uri
- + ";listen start select prefix SelectionChanged url " + uri, false);
+ + ";listen start select prefix SelectionChanged url " + uri,
+ false);
}
/**
{
chimera = null;
currentModelsMap.clear();
- this.chimeraRestPort = 0;
+ this.chimeraRestPort = 0;
structureManager.clearOnChimeraExit();
}
} catch (Exception e)
{
logger.error("Failed to get REST port number from " + responses
- + ": "
- + e.getMessage());
+ + ": " + e.getMessage());
} finally
{
try
*/
public List<String> sendChimeraCommand(String command, boolean reply)
{
-// System.out.println("chimeradebug>> " + command);
+ // System.out.println("chimeradebug>> " + command);
if (!isChimeraLaunched() || command == null
|| "".equals(command.trim()))
{
List<String> reply = new ArrayList<String>();
BufferedReader response = null;
- try {
+ try
+ {
response = HttpClientUtils
.doHttpUrlPost(restUrl, commands, 100, 5000);
String line = "";
- while ((line = response.readLine()) != null) {
+ while ((line = response.readLine()) != null)
+ {
reply.add(line);
}
} catch (Exception e)
import java.awt.Color;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
/**
- * This class provides the implementation for the ChimeraModel, ChimeraChain, and ChimeraResidue
- * objects
+ * This class provides the implementation for the ChimeraModel, ChimeraChain,
+ * and ChimeraResidue objects
*
* @author scooter
*
*/
-public class ChimeraModel implements ChimeraStructuralObject {
-
- private String name; // The name of this model
- private ModelType type; // The type of the model
- private int modelNumber; // The model number
- private int subModelNumber; // The sub-model number
-
- private Color modelColor = null; // The color of this model (from Chimera)
- private Object userData = null; // User data associated with this model
- private boolean selected = false; // The selected state of this model
-
- private TreeMap<String, ChimeraChain> chainMap; // The list of chains
- // private TreeMap<String, ChimeraResidue> residueMap; // The list of residues
- private HashSet<ChimeraResidue> funcResidues; // List of functional residues
-
- /**
- * Constructor to create a model
- *
- * @param name
- * the name of this model
- * @param color
- * the model Color
- * @param modelNumber
- * the model number
- * @param subModelNumber
- * the sub-model number
- */
- public ChimeraModel(String name, ModelType type, int modelNumber, int subModelNumber) {
- this.name = name;
- this.type = type;
- this.modelNumber = modelNumber;
- this.subModelNumber = subModelNumber;
-
- this.chainMap = new TreeMap<String, ChimeraChain>();
- this.funcResidues = new HashSet<ChimeraResidue>();
- }
-
- /**
- * Constructor to create a model from the Chimera input line
- *
- * @param inputLine
- * Chimera input line from which to construct this model
- */
- // TODO: [Optional] How to distinguish between PDB and MODBASE?
- // invoked when listing models: listm type molecule; lists level molecule
- // line = model id #0 type Molecule name 1ert
- public ChimeraModel(String inputLine) {
- this.name = ChimUtils.parseModelName(inputLine);
- // TODO: [Optional] Write a separate method to get model type
- if (name.startsWith("smiles")) {
- this.type = ModelType.SMILES;
- } else {
- this.type = ModelType.PDB_MODEL;
- }
- this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0];
- this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1];
-
- this.chainMap = new TreeMap<String, ChimeraChain>();
- this.funcResidues = new HashSet<ChimeraResidue>();
- }
-
- /**
- * Add a residue to this model
- *
- * @param residue
- * to add to the model
- */
- public void addResidue(ChimeraResidue residue) {
- residue.setChimeraModel(this);
- // residueMap.put(residue.getIndex(), residue);
- String chainId = residue.getChainId();
- if (chainId != null) {
- addResidue(chainId, residue);
- } else {
- addResidue("_", residue);
- }
- // Put it in our map so that we can return it in order
- // residueMap.put(residue.getIndex(), residue);
- }
-
- /**
- * Add a residue to a chain in this model. If the chain associated with chainId doesn't exist,
- * it will be created.
- *
- * @param chainId
- * to add the residue to
- * @param residue
- * to add to the chain
- */
- public void addResidue(String chainId, ChimeraResidue residue) {
- ChimeraChain chain = null;
- if (!chainMap.containsKey(chainId)) {
- chain = new ChimeraChain(this.modelNumber, this.subModelNumber, chainId);
- chain.setChimeraModel(this);
- chainMap.put(chainId, chain);
- } else {
- chain = chainMap.get(chainId);
- }
- chain.addResidue(residue);
- }
-
- /**
- * Get the ChimeraModel (required for ChimeraStructuralObject interface)
- *
- * @return ChimeraModel
- */
- public ChimeraModel getChimeraModel() {
- return this;
- }
-
- /**
- * Get the model color of this model
- *
- * @return model color of this model
- */
- public Color getModelColor() {
- return this.modelColor;
- }
-
- /**
- * Set the color of this model
- *
- * @param color
- * Color of this model
- */
- public void setModelColor(Color color) {
- this.modelColor = color;
- }
-
- /**
- * Return the name of this model
- *
- * @return model name
- */
- public String getModelName() {
- return name;
- }
-
- /**
- * Set the name of this model
- *
- * @param name
- * model name
- */
- public void setModelName(String name) {
- this.name = name;
- }
-
- /**
- * Get the model number of this model
- *
- * @return integer model number
- */
- public int getModelNumber() {
- return modelNumber;
- }
-
- /**
- * Set the model number of this model
- *
- * @param modelNumber
- * integer model number
- */
- public void setModelNumber(int modelNumber) {
- this.modelNumber = modelNumber;
- }
-
- /**
- * Get the sub-model number of this model
- *
- * @return integer sub-model number
- */
- public int getSubModelNumber() {
- return subModelNumber;
- }
-
- /**
- * Set the sub-model number of this model
- *
- * @param subModelNumber
- * integer model number
- */
- public void setSubModelNumber(int subModelNumber) {
- this.subModelNumber = subModelNumber;
- }
-
- public ModelType getModelType() {
- return type;
- }
-
- public void setModelType(ModelType type) {
- this.type = type;
- }
-
- public HashSet<ChimeraResidue> getFuncResidues() {
- return funcResidues;
- }
-
- public void setFuncResidues(List<String> residues) {
- for (String residue : residues) {
- for (ChimeraChain chain : getChains()) {
- if (residue.indexOf("-") > 0) {
- funcResidues.addAll(chain.getResidueRange(residue));
- } else {
- funcResidues.add(chain.getResidue(residue));
- }
- }
- }
- }
-
- /**
- * Get the user data for this model
- *
- * @return user data
- */
- public Object getUserData() {
- return userData;
- }
-
- /**
- * Set the user data for this model
- *
- * @param data
- * user data to associate with this model
- */
- public void setUserData(Object data) {
- this.userData = data;
- }
-
- /**
- * Return the selected state of this model
- *
- * @return the selected state
- */
- public boolean isSelected() {
- return selected;
- }
-
- /**
- * Set the selected state of this model
- *
- * @param selected
- * a boolean to set the selected state to
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
-
- /**
- * Return the chains in this model as a List
- *
- * @return the chains in this model as a list
- */
- public List<ChimeraStructuralObject> getChildren() {
- return new ArrayList<ChimeraStructuralObject>(chainMap.values());
- }
-
- /**
- * Return the chains in this model as a colleciton
- *
- * @return the chains in this model
- */
- public Collection<ChimeraChain> getChains() {
- return chainMap.values();
- }
-
- /**
- * Get the number of chains in this model
- *
- * @return integer chain count
- */
- public int getChainCount() {
- return chainMap.size();
- }
-
- /**
- * Get the list of chain names associated with this model
- *
- * @return return the list of chain names for this model
- */
- public Collection<String> getChainNames() {
- return chainMap.keySet();
- }
-
- /**
- * Get the residues associated with this model
- *
- * @return the list of residues in this model
- */
- public Collection<ChimeraResidue> getResidues() {
- Collection<ChimeraResidue> residues = new ArrayList<ChimeraResidue>();
- for (ChimeraChain chain : getChains()) {
- residues.addAll(chain.getResidues());
- }
- return residues;
- }
-
- /**
- * Get the number of residues in this model
- *
- * @return integer residues count
- */
- public int getResidueCount() {
- int count = 0;
- for (ChimeraChain chain : getChains()) {
- count += chain.getResidueCount();
- }
- return count;
- }
-
- /**
- * Get a specific chain from the model
- *
- * @param chain
- * the ID of the chain to return
- * @return ChimeraChain associated with the chain
- */
- public ChimeraChain getChain(String chain) {
- if (chainMap.containsKey(chain)) {
- return chainMap.get(chain);
- }
- return null;
- }
-
- /**
- * Return a specific residue based on its index
- *
- * @param index
- * of the residue to return
- * @return the residue associated with that index
- */
- public ChimeraResidue getResidue(String chainId, String index) {
- if (chainMap.containsKey(chainId)) {
- return chainMap.get(chainId).getResidue(index);
- }
- return null;
- }
-
- /**
- * Checks if this model has selected children.
- */
- public boolean hasSelectedChildren() {
- if (selected) {
- return true;
- } else {
- for (ChimeraChain chain : getChains()) {
- if (chain.hasSelectedChildren()) {
- return true;
- }
- }
- }
- return false;
- }
-
- /**
- * Return the list of selected residues
- *
- * @return all selected residues
- */
- public List<ChimeraResidue> getSelectedResidues() {
- List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
- for (ChimeraChain chain : getChains()) {
- if (selected) {
- residueList.addAll(chain.getSelectedResidues());
- } else {
- residueList.addAll(getResidues());
- }
- }
- return residueList;
- }
-
-
- /**
- * Return the Chimera specification for this model.
- */
- public String toSpec() {
- if (subModelNumber == 0)
- return ("#" + modelNumber);
- return ("#" + modelNumber + "." + subModelNumber);
- }
-
- /**
- * Return a string representation for the model. Shorten if longer than 100 characters.
- */
- public String toString() {
- String modelName = "";
- // TODO: [Optional] Change cutoff for shortening model names in the structure naviagator dialog
- if (getChainCount() > 0) {
- modelName = "Model " + toSpec() + " " + name + " (" + getChainCount() + " chains, "
- + getResidueCount() + " residues)";
- } else if (getResidueCount() > 0) {
- modelName = "Model " + toSpec() + " " + name + " (" + getResidueCount() + " residues)";
- } else {
- modelName = "Model " + toSpec() + " " + name + "";
- }
-
- Set<String> networkNames = new HashSet<String>();
- Set<String> nodeNames = new HashSet<String>();
- Set<String> edgeNames = new HashSet<String>();
-
- String cytoName = " [";
- if (networkNames.size() > 0) {
- if (networkNames.size() == 1) {
- cytoName += "Network {";
- } else if (networkNames.size() > 1) {
- cytoName += "Networks {";
- }
- for (String cName : networkNames) {
- cytoName += cName + ",";
- }
- cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
- }
- if (nodeNames.size() > 0) {
- if (nodeNames.size() == 1) {
- cytoName += "Node {";
- } else if (nodeNames.size() > 1) {
- cytoName += "Nodes {";
- }
- for (String cName : nodeNames) {
- cytoName += cName + ",";
- }
- cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
- }
- if (edgeNames.size() > 0) {
- if (edgeNames.size() == 1) {
- cytoName += "Edge {";
- } else if (edgeNames.size() > 1) {
- cytoName += "Edges {";
- }
- for (String cName : edgeNames) {
- cytoName += cName + ",";
- }
- cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
- }
- if (cytoName.endsWith(", ")) {
- cytoName = cytoName.substring(0, cytoName.length() - 2);
- }
- cytoName += "]";
- String nodeName = modelName + cytoName;
- if (nodeName.length() > 100) {
- nodeName = nodeName.substring(0, 100) + "...";
- }
- return nodeName;
- }
+public class ChimeraModel implements ChimeraStructuralObject
+{
+
+ private String name; // The name of this model
+
+ private ModelType type; // The type of the model
+
+ private int modelNumber; // The model number
+
+ private int subModelNumber; // The sub-model number
+
+ private Color modelColor = null; // The color of this model (from Chimera)
+
+ private Object userData = null; // User data associated with this model
+
+ private boolean selected = false; // The selected state of this model
+
+ private TreeMap<String, ChimeraChain> chainMap; // The list of chains
+
+ // private TreeMap<String, ChimeraResidue> residueMap; // The list of residues
+ private HashSet<ChimeraResidue> funcResidues; // List of functional residues
+
+ /**
+ * Constructor to create a model
+ *
+ * @param name
+ * the name of this model
+ * @param color
+ * the model Color
+ * @param modelNumber
+ * the model number
+ * @param subModelNumber
+ * the sub-model number
+ */
+ public ChimeraModel(String name, ModelType type, int modelNumber,
+ int subModelNumber)
+ {
+ this.name = name;
+ this.type = type;
+ this.modelNumber = modelNumber;
+ this.subModelNumber = subModelNumber;
+
+ this.chainMap = new TreeMap<String, ChimeraChain>();
+ this.funcResidues = new HashSet<ChimeraResidue>();
+ }
+
+ /**
+ * Constructor to create a model from the Chimera input line
+ *
+ * @param inputLine
+ * Chimera input line from which to construct this model
+ */
+ // TODO: [Optional] How to distinguish between PDB and MODBASE?
+ // invoked when listing models: listm type molecule; lists level molecule
+ // line = model id #0 type Molecule name 1ert
+ public ChimeraModel(String inputLine)
+ {
+ this.name = ChimUtils.parseModelName(inputLine);
+ // TODO: [Optional] Write a separate method to get model type
+ if (name.startsWith("smiles"))
+ {
+ this.type = ModelType.SMILES;
+ }
+ else
+ {
+ this.type = ModelType.PDB_MODEL;
+ }
+ this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0];
+ this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1];
+
+ this.chainMap = new TreeMap<String, ChimeraChain>();
+ this.funcResidues = new HashSet<ChimeraResidue>();
+ }
+
+ /**
+ * Add a residue to this model
+ *
+ * @param residue
+ * to add to the model
+ */
+ public void addResidue(ChimeraResidue residue)
+ {
+ residue.setChimeraModel(this);
+ // residueMap.put(residue.getIndex(), residue);
+ String chainId = residue.getChainId();
+ if (chainId != null)
+ {
+ addResidue(chainId, residue);
+ }
+ else
+ {
+ addResidue("_", residue);
+ }
+ // Put it in our map so that we can return it in order
+ // residueMap.put(residue.getIndex(), residue);
+ }
+
+ /**
+ * Add a residue to a chain in this model. If the chain associated with
+ * chainId doesn't exist, it will be created.
+ *
+ * @param chainId
+ * to add the residue to
+ * @param residue
+ * to add to the chain
+ */
+ public void addResidue(String chainId, ChimeraResidue residue)
+ {
+ ChimeraChain chain = null;
+ if (!chainMap.containsKey(chainId))
+ {
+ chain = new ChimeraChain(this.modelNumber, this.subModelNumber,
+ chainId);
+ chain.setChimeraModel(this);
+ chainMap.put(chainId, chain);
+ }
+ else
+ {
+ chain = chainMap.get(chainId);
+ }
+ chain.addResidue(residue);
+ }
+
+ /**
+ * Get the ChimeraModel (required for ChimeraStructuralObject interface)
+ *
+ * @return ChimeraModel
+ */
+ public ChimeraModel getChimeraModel()
+ {
+ return this;
+ }
+
+ /**
+ * Get the model color of this model
+ *
+ * @return model color of this model
+ */
+ public Color getModelColor()
+ {
+ return this.modelColor;
+ }
+
+ /**
+ * Set the color of this model
+ *
+ * @param color
+ * Color of this model
+ */
+ public void setModelColor(Color color)
+ {
+ this.modelColor = color;
+ }
+
+ /**
+ * Return the name of this model
+ *
+ * @return model name
+ */
+ public String getModelName()
+ {
+ return name;
+ }
+
+ /**
+ * Set the name of this model
+ *
+ * @param name
+ * model name
+ */
+ public void setModelName(String name)
+ {
+ this.name = name;
+ }
+
+ /**
+ * Get the model number of this model
+ *
+ * @return integer model number
+ */
+ public int getModelNumber()
+ {
+ return modelNumber;
+ }
+
+ /**
+ * Set the model number of this model
+ *
+ * @param modelNumber
+ * integer model number
+ */
+ public void setModelNumber(int modelNumber)
+ {
+ this.modelNumber = modelNumber;
+ }
+
+ /**
+ * Get the sub-model number of this model
+ *
+ * @return integer sub-model number
+ */
+ public int getSubModelNumber()
+ {
+ return subModelNumber;
+ }
+
+ /**
+ * Set the sub-model number of this model
+ *
+ * @param subModelNumber
+ * integer model number
+ */
+ public void setSubModelNumber(int subModelNumber)
+ {
+ this.subModelNumber = subModelNumber;
+ }
+
+ public ModelType getModelType()
+ {
+ return type;
+ }
+
+ public void setModelType(ModelType type)
+ {
+ this.type = type;
+ }
+
+ public HashSet<ChimeraResidue> getFuncResidues()
+ {
+ return funcResidues;
+ }
+
+ public void setFuncResidues(List<String> residues)
+ {
+ for (String residue : residues)
+ {
+ for (ChimeraChain chain : getChains())
+ {
+ if (residue.indexOf("-") > 0)
+ {
+ funcResidues.addAll(chain.getResidueRange(residue));
+ }
+ else
+ {
+ funcResidues.add(chain.getResidue(residue));
+ }
+ }
+ }
+ }
+
+ /**
+ * Get the user data for this model
+ *
+ * @return user data
+ */
+ public Object getUserData()
+ {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this model
+ *
+ * @param data
+ * user data to associate with this model
+ */
+ public void setUserData(Object data)
+ {
+ this.userData = data;
+ }
+
+ /**
+ * Return the selected state of this model
+ *
+ * @return the selected state
+ */
+ public boolean isSelected()
+ {
+ return selected;
+ }
+
+ /**
+ * Set the selected state of this model
+ *
+ * @param selected
+ * a boolean to set the selected state to
+ */
+ public void setSelected(boolean selected)
+ {
+ this.selected = selected;
+ }
+
+ /**
+ * Return the chains in this model as a List
+ *
+ * @return the chains in this model as a list
+ */
+ public List<ChimeraStructuralObject> getChildren()
+ {
+ return new ArrayList<ChimeraStructuralObject>(chainMap.values());
+ }
+
+ /**
+ * Return the chains in this model as a colleciton
+ *
+ * @return the chains in this model
+ */
+ public Collection<ChimeraChain> getChains()
+ {
+ return chainMap.values();
+ }
+
+ /**
+ * Get the number of chains in this model
+ *
+ * @return integer chain count
+ */
+ public int getChainCount()
+ {
+ return chainMap.size();
+ }
+
+ /**
+ * Get the list of chain names associated with this model
+ *
+ * @return return the list of chain names for this model
+ */
+ public Collection<String> getChainNames()
+ {
+ return chainMap.keySet();
+ }
+
+ /**
+ * Get the residues associated with this model
+ *
+ * @return the list of residues in this model
+ */
+ public Collection<ChimeraResidue> getResidues()
+ {
+ Collection<ChimeraResidue> residues = new ArrayList<ChimeraResidue>();
+ for (ChimeraChain chain : getChains())
+ {
+ residues.addAll(chain.getResidues());
+ }
+ return residues;
+ }
+
+ /**
+ * Get the number of residues in this model
+ *
+ * @return integer residues count
+ */
+ public int getResidueCount()
+ {
+ int count = 0;
+ for (ChimeraChain chain : getChains())
+ {
+ count += chain.getResidueCount();
+ }
+ return count;
+ }
+
+ /**
+ * Get a specific chain from the model
+ *
+ * @param chain
+ * the ID of the chain to return
+ * @return ChimeraChain associated with the chain
+ */
+ public ChimeraChain getChain(String chain)
+ {
+ if (chainMap.containsKey(chain))
+ {
+ return chainMap.get(chain);
+ }
+ return null;
+ }
+
+ /**
+ * Return a specific residue based on its index
+ *
+ * @param index
+ * of the residue to return
+ * @return the residue associated with that index
+ */
+ public ChimeraResidue getResidue(String chainId, String index)
+ {
+ if (chainMap.containsKey(chainId))
+ {
+ return chainMap.get(chainId).getResidue(index);
+ }
+ return null;
+ }
+
+ /**
+ * Checks if this model has selected children.
+ */
+ public boolean hasSelectedChildren()
+ {
+ if (selected)
+ {
+ return true;
+ }
+ else
+ {
+ for (ChimeraChain chain : getChains())
+ {
+ if (chain.hasSelectedChildren())
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Return the list of selected residues
+ *
+ * @return all selected residues
+ */
+ public List<ChimeraResidue> getSelectedResidues()
+ {
+ List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
+ for (ChimeraChain chain : getChains())
+ {
+ if (selected)
+ {
+ residueList.addAll(chain.getSelectedResidues());
+ }
+ else
+ {
+ residueList.addAll(getResidues());
+ }
+ }
+ return residueList;
+ }
+
+ /**
+ * Return the Chimera specification for this model.
+ */
+ public String toSpec()
+ {
+ if (subModelNumber == 0)
+ return ("#" + modelNumber);
+ return ("#" + modelNumber + "." + subModelNumber);
+ }
+
+ /**
+ * Return a string representation for the model. Shorten if longer than 100
+ * characters.
+ */
+ public String toString()
+ {
+ String modelName = "";
+ // TODO: [Optional] Change cutoff for shortening model names in the
+ // structure naviagator dialog
+ if (getChainCount() > 0)
+ {
+ modelName = "Model " + toSpec() + " " + name + " (" + getChainCount()
+ + " chains, " + getResidueCount() + " residues)";
+ }
+ else if (getResidueCount() > 0)
+ {
+ modelName = "Model " + toSpec() + " " + name + " ("
+ + getResidueCount() + " residues)";
+ }
+ else
+ {
+ modelName = "Model " + toSpec() + " " + name + "";
+ }
+
+ Set<String> networkNames = new HashSet<String>();
+ Set<String> nodeNames = new HashSet<String>();
+ Set<String> edgeNames = new HashSet<String>();
+
+ String cytoName = " [";
+ if (networkNames.size() > 0)
+ {
+ if (networkNames.size() == 1)
+ {
+ cytoName += "Network {";
+ }
+ else if (networkNames.size() > 1)
+ {
+ cytoName += "Networks {";
+ }
+ for (String cName : networkNames)
+ {
+ cytoName += cName + ",";
+ }
+ cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+ }
+ if (nodeNames.size() > 0)
+ {
+ if (nodeNames.size() == 1)
+ {
+ cytoName += "Node {";
+ }
+ else if (nodeNames.size() > 1)
+ {
+ cytoName += "Nodes {";
+ }
+ for (String cName : nodeNames)
+ {
+ cytoName += cName + ",";
+ }
+ cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+ }
+ if (edgeNames.size() > 0)
+ {
+ if (edgeNames.size() == 1)
+ {
+ cytoName += "Edge {";
+ }
+ else if (edgeNames.size() > 1)
+ {
+ cytoName += "Edges {";
+ }
+ for (String cName : edgeNames)
+ {
+ cytoName += cName + ",";
+ }
+ cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+ }
+ if (cytoName.endsWith(", "))
+ {
+ cytoName = cytoName.substring(0, cytoName.length() - 2);
+ }
+ cytoName += "]";
+ String nodeName = modelName + cytoName;
+ if (nodeName.length() > 100)
+ {
+ nodeName = nodeName.substring(0, 100) + "...";
+ }
+ return nodeName;
+ }
}
*
*/
-public class ChimeraResidue implements ChimeraStructuralObject, Comparable<ChimeraResidue> {
-
- /* Constants */
- public static final int SINGLE_LETTER = 0; // Display residues as a single
- // letter
- public static final int THREE_LETTER = 1; // Display residues as three letters
- public static final int FULL_NAME = 2; // Display full residue names
-
- private String type; // Residue type
- private String index; // Residue index
- private String chainId; // ChainID for this residue
- private int modelNumber; // model number for this residue
- private int subModelNumber; // sub-model number for this residue
- protected int residueNumber;
- protected String insertionCode;
- private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
- private Object userData; // user data to associate with this residue
- // public static HashMap<String, String> aaNames = null; // a map of amino acid
- // names
- private static int displayType = THREE_LETTER; // the current display type
- private boolean selected = false; // the selection state
-
- /**
- * Constructor to create a new ChimeraResidue
- *
- * @param type
- * the residue type
- * @param index
- * the index of the residue
- * @param modelNumber
- * the model number this residue is part of
- */
- public ChimeraResidue(String type, String index, int modelNumber) {
- this(type, index, modelNumber, 0);
- }
-
- /**
- * Constructor to create a new ChimeraResidue
- *
- * @param type
- * the residue type
- * @param index
- * the index of the residue
- * @param modelNumber
- * the model number this residue is part of
- * @param subModelNumber
- * the sub-model number this residue is part of
- */
- public ChimeraResidue(String type, String index, int modelNumber, int subModelNumber) {
- this.type = type;
- this.index = index;
- this.modelNumber = modelNumber;
- this.subModelNumber = subModelNumber;
- splitInsertionCode(this.index);
- // if (aaNames == null) {
- // initNames();
- // }
- }
-
- /**
- * Constructor to create a new ChimeraResidue from an input line
- *
- * @param chimeraInputLine
- * a Chimera residue description
- */
- // invoked when listing (selected) residues: listr spec #0; lists level residue
- // Line: residue id #0:37.A type MET
- public ChimeraResidue(String chimeraInputLine) {
- // initNames();
- String[] split1 = chimeraInputLine.split(":");
-
- // First half has model number -- get the number
- int numberOffset = split1[0].indexOf('#');
- String model = split1[0].substring(numberOffset + 1);
- int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
- try {
- this.subModelNumber = 0;
- if (decimalOffset > 0) {
- this.subModelNumber = Integer.parseInt(model.substring(decimalOffset + 1));
- this.modelNumber = Integer.parseInt(model.substring(0, decimalOffset));
- } else {
- this.modelNumber = Integer.parseInt(model);
- }
- } catch (Exception e) {
- LoggerFactory.getLogger(ChimeraResidue.class)
- .error("Unexpected return from Chimera: " + model);
- this.modelNumber = -1;
- }
-
- // Second half has residue info: index & type
- String[] rTokens = split1[1].split(" ");
- this.type = rTokens[2];
-
- String[] iTokens = rTokens[0].split("\\.");
- if (iTokens.length > 0) {
- this.index = iTokens[0];
-
- // Careful, might or might not have a chainID
- if (iTokens.length > 1)
- this.chainId = iTokens[1];
- else
- this.chainId = "_";
- } else
- this.index = rTokens[0];
-
- splitInsertionCode(this.index);
- }
-
- /**
- * Set the selected state for this residue
- *
- * @param selected
- * the selection state to set
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
-
- /**
- * Return the selected state of this residue
- *
- * @return the selected state
- */
- public boolean isSelected() {
- return selected;
- }
-
- /**
- * Return an array made up of this residue (required for ChimeraStructuralObject interface
- *
- * @return a List with this residue as its sole member
- */
- public List<ChimeraStructuralObject> getChildren() {
- List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
- v.add(this);
- return v;
- }
-
- /**
- * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
- * where <i>residue_name</i> could be either the single letter, three letter, or full name
- * representation of the amino acid.
- *
- * @return the string representation
- */
- public String displayName() {
- return toString();
- }
-
- /**
- * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
- * where <i>residue_name</i> could be either the single letter, three letter, or full name
- * representation of the amino acid.
- *
- * @return the string representation
- */
- public String toString() {
- if (displayType == FULL_NAME) {
- return (ChimUtils.toFullName(type) + " " + index);
- } else if (displayType == SINGLE_LETTER) {
- return (ChimUtils.toSingleLetter(type) + " " + index);
- } else if (displayType == THREE_LETTER) {
- return (ChimUtils.toThreeLetter(type) + " " + index);
- } else {
- return (type + " " + index);
- }
- }
-
- /**
- * Return the Chimera specification for this Residue
- *
- * @return Chimera specification
- */
- public String toSpec() {
- if (!chainId.equals("_"))
- return ("#" + modelNumber + ":" + index + "." + chainId);
- else
- return ("#" + modelNumber + ":" + index + ".");
- }
-
- /**
- * Get the index of this residue
- *
- * @return residue index
- */
- public String getIndex() {
- return this.index;
- }
-
- /**
- * Get the chainID for this residue
- *
- * @return String value of the chainId
- */
- public String getChainId() {
- return this.chainId;
- }
-
- /**
- * Get the type for this residue
- *
- * @return residue type
- */
- public String getType() {
- return this.type;
- }
-
- /**
- * Get the model number for this residue
- *
- * @return the model number
- */
- public int getModelNumber() {
- return this.modelNumber;
- }
-
- /**
- * Get the sub-model number for this residue
- *
- * @return the sub-model number
- */
- public int getSubModelNumber() {
- return this.subModelNumber;
- }
-
- /**
- * Get the model this residue is part of
- *
- * @return the ChimeraModel
- */
- public ChimeraModel getChimeraModel() {
- return this.chimeraModel;
- }
-
- /**
- * Set the model this residue is part of
- *
- * @param chimeraModel
- * the ChimeraModel this model is part of
- */
- public void setChimeraModel(ChimeraModel chimeraModel) {
- this.chimeraModel = chimeraModel;
- }
-
- /**
- * Get the user data for this residue
- *
- * @return user data
- */
- public Object getUserData() {
- return userData;
- }
-
- /**
- * Set the user data for this Residue
- *
- * @param data
- * the user data to associate with this residue
- */
- public void setUserData(Object data) {
- this.userData = data;
- }
-
- public int compareTo(ChimeraResidue c2) {
- if (residueNumber < c2.residueNumber)
- return -1;
- else if (residueNumber == c2.residueNumber) {
- if (insertionCode == null && c2.insertionCode == null)
- return 0;
- else if (insertionCode == null)
- return -1;
- else if (c2.insertionCode == null)
- return 1;
- return (insertionCode.compareTo(c2.insertionCode));
- }
- return 1;
- }
-
- public void splitInsertionCode(String residue) {
- // OK, split the index into number and insertion code
- Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
- Matcher m = p.matcher(residue);
- if (m.matches()) {
- this.residueNumber = Integer.parseInt(m.group(1));
- if (m.groupCount() > 1)
- this.insertionCode = m.group(2);
- else
- this.insertionCode = null;
- }
- }
-
- /**********************************************
- * Static routines
- *********************************************/
-
- /**
- * Initialize the residue names
- */
- // private static void initNames() {
- // // Create our residue name table
- // aaNames = new HashMap<String, String>();
- // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
- // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
- // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
- // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
- // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
- // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
- // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
- // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
- // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
- // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
- // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
- // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
- // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
- // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
- // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
- // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
- // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
- // aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
- // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
- // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
- // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
- // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
- // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
- // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
- // }
-
- /**
- * Set the display type.
- *
- * @param type
- * the display type
- */
- public static void setDisplayType(int type) {
- displayType = type;
- }
-
- public static int getDisplayType() {
- return displayType;
- }
-
- public boolean hasSelectedChildren() {
- return false;
- }
+public class ChimeraResidue implements ChimeraStructuralObject,
+ Comparable<ChimeraResidue>
+{
+
+ /* Constants */
+ public static final int SINGLE_LETTER = 0; // Display residues as a single
+ // letter
+
+ public static final int THREE_LETTER = 1; // Display residues as three letters
+
+ public static final int FULL_NAME = 2; // Display full residue names
+
+ private String type; // Residue type
+
+ private String index; // Residue index
+
+ private String chainId; // ChainID for this residue
+
+ private int modelNumber; // model number for this residue
+
+ private int subModelNumber; // sub-model number for this residue
+
+ protected int residueNumber;
+
+ protected String insertionCode;
+
+ private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
+
+ private Object userData; // user data to associate with this residue
+
+ // public static HashMap<String, String> aaNames = null; // a map of amino
+ // acid
+ // names
+ private static int displayType = THREE_LETTER; // the current display type
+
+ private boolean selected = false; // the selection state
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber)
+ {
+ this(type, index, modelNumber, 0);
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ * @param subModelNumber
+ * the sub-model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber,
+ int subModelNumber)
+ {
+ this.type = type;
+ this.index = index;
+ this.modelNumber = modelNumber;
+ this.subModelNumber = subModelNumber;
+ splitInsertionCode(this.index);
+ // if (aaNames == null) {
+ // initNames();
+ // }
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue from an input line
+ *
+ * @param chimeraInputLine
+ * a Chimera residue description
+ */
+ // invoked when listing (selected) residues: listr spec #0; lists level
+ // residue
+ // Line: residue id #0:37.A type MET
+ public ChimeraResidue(String chimeraInputLine)
+ {
+ // initNames();
+ String[] split1 = chimeraInputLine.split(":");
+
+ // First half has model number -- get the number
+ int numberOffset = split1[0].indexOf('#');
+ String model = split1[0].substring(numberOffset + 1);
+ int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
+ try
+ {
+ this.subModelNumber = 0;
+ if (decimalOffset > 0)
+ {
+ this.subModelNumber = Integer.parseInt(model
+ .substring(decimalOffset + 1));
+ this.modelNumber = Integer.parseInt(model.substring(0,
+ decimalOffset));
+ }
+ else
+ {
+ this.modelNumber = Integer.parseInt(model);
+ }
+ } catch (Exception e)
+ {
+ LoggerFactory.getLogger(ChimeraResidue.class).error(
+ "Unexpected return from Chimera: " + model);
+ this.modelNumber = -1;
+ }
+
+ // Second half has residue info: index & type
+ String[] rTokens = split1[1].split(" ");
+ this.type = rTokens[2];
+
+ String[] iTokens = rTokens[0].split("\\.");
+ if (iTokens.length > 0)
+ {
+ this.index = iTokens[0];
+
+ // Careful, might or might not have a chainID
+ if (iTokens.length > 1)
+ this.chainId = iTokens[1];
+ else
+ this.chainId = "_";
+ }
+ else
+ this.index = rTokens[0];
+
+ splitInsertionCode(this.index);
+ }
+
+ /**
+ * Set the selected state for this residue
+ *
+ * @param selected
+ * the selection state to set
+ */
+ public void setSelected(boolean selected)
+ {
+ this.selected = selected;
+ }
+
+ /**
+ * Return the selected state of this residue
+ *
+ * @return the selected state
+ */
+ public boolean isSelected()
+ {
+ return selected;
+ }
+
+ /**
+ * Return an array made up of this residue (required for
+ * ChimeraStructuralObject interface
+ *
+ * @return a List with this residue as its sole member
+ */
+ public List<ChimeraStructuralObject> getChildren()
+ {
+ List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
+ v.add(this);
+ return v;
+ }
+
+ /**
+ * Return the string representation of this residue as follows:
+ * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
+ * either the single letter, three letter, or full name representation of the
+ * amino acid.
+ *
+ * @return the string representation
+ */
+ public String displayName()
+ {
+ return toString();
+ }
+
+ /**
+ * Return the string representation of this residue as follows:
+ * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
+ * either the single letter, three letter, or full name representation of the
+ * amino acid.
+ *
+ * @return the string representation
+ */
+ public String toString()
+ {
+ if (displayType == FULL_NAME)
+ {
+ return (ChimUtils.toFullName(type) + " " + index);
+ }
+ else if (displayType == SINGLE_LETTER)
+ {
+ return (ChimUtils.toSingleLetter(type) + " " + index);
+ }
+ else if (displayType == THREE_LETTER)
+ {
+ return (ChimUtils.toThreeLetter(type) + " " + index);
+ }
+ else
+ {
+ return (type + " " + index);
+ }
+ }
+
+ /**
+ * Return the Chimera specification for this Residue
+ *
+ * @return Chimera specification
+ */
+ public String toSpec()
+ {
+ if (!chainId.equals("_"))
+ return ("#" + modelNumber + ":" + index + "." + chainId);
+ else
+ return ("#" + modelNumber + ":" + index + ".");
+ }
+
+ /**
+ * Get the index of this residue
+ *
+ * @return residue index
+ */
+ public String getIndex()
+ {
+ return this.index;
+ }
+
+ /**
+ * Get the chainID for this residue
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId()
+ {
+ return this.chainId;
+ }
+
+ /**
+ * Get the type for this residue
+ *
+ * @return residue type
+ */
+ public String getType()
+ {
+ return this.type;
+ }
+
+ /**
+ * Get the model number for this residue
+ *
+ * @return the model number
+ */
+ public int getModelNumber()
+ {
+ return this.modelNumber;
+ }
+
+ /**
+ * Get the sub-model number for this residue
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber()
+ {
+ return this.subModelNumber;
+ }
+
+ /**
+ * Get the model this residue is part of
+ *
+ * @return the ChimeraModel
+ */
+ public ChimeraModel getChimeraModel()
+ {
+ return this.chimeraModel;
+ }
+
+ /**
+ * Set the model this residue is part of
+ *
+ * @param chimeraModel
+ * the ChimeraModel this model is part of
+ */
+ public void setChimeraModel(ChimeraModel chimeraModel)
+ {
+ this.chimeraModel = chimeraModel;
+ }
+
+ /**
+ * Get the user data for this residue
+ *
+ * @return user data
+ */
+ public Object getUserData()
+ {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this Residue
+ *
+ * @param data
+ * the user data to associate with this residue
+ */
+ public void setUserData(Object data)
+ {
+ this.userData = data;
+ }
+
+ public int compareTo(ChimeraResidue c2)
+ {
+ if (residueNumber < c2.residueNumber)
+ return -1;
+ else if (residueNumber == c2.residueNumber)
+ {
+ if (insertionCode == null && c2.insertionCode == null)
+ return 0;
+ else if (insertionCode == null)
+ return -1;
+ else if (c2.insertionCode == null)
+ return 1;
+ return (insertionCode.compareTo(c2.insertionCode));
+ }
+ return 1;
+ }
+
+ public void splitInsertionCode(String residue)
+ {
+ // OK, split the index into number and insertion code
+ Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
+ Matcher m = p.matcher(residue);
+ if (m.matches())
+ {
+ this.residueNumber = Integer.parseInt(m.group(1));
+ if (m.groupCount() > 1)
+ this.insertionCode = m.group(2);
+ else
+ this.insertionCode = null;
+ }
+ }
+
+ /**********************************************
+ * Static routines
+ *********************************************/
+
+ /**
+ * Initialize the residue names
+ */
+ // private static void initNames() {
+ // // Create our residue name table
+ // aaNames = new HashMap<String, String>();
+ // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+ // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+ // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+ // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+ // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+ // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+ // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+ // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+ // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+ // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+ // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+ // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+ // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+ // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+ // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+ // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+ // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+ // aaNames.put("TRP",
+ // "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+ // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+ // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+ // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+ // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+ // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+ // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+ // }
+
+ /**
+ * Set the display type.
+ *
+ * @param type
+ * the display type
+ */
+ public static void setDisplayType(int type)
+ {
+ displayType = type;
+ }
+
+ public static int getDisplayType()
+ {
+ return displayType;
+ }
+
+ public boolean hasSelectedChildren()
+ {
+ return false;
+ }
}
*/
package ext.edu.ucsf.rbvi.strucviz2;
-import java.lang.String;
import java.util.List;
/**
- * This interface provides a common set of methods that are implemented by the ChimeraModel,
- * ChimeraChain, and ChimeraResidue classes.
+ * This interface provides a common set of methods that are implemented by the
+ * ChimeraModel, ChimeraChain, and ChimeraResidue classes.
*
* @author scooter
*
*/
-public interface ChimeraStructuralObject {
+public interface ChimeraStructuralObject
+{
- /**
- * Return the Chimera selection specification for this object
- *
- * @return a String representing a Chimera atom-spec
- */
- public String toSpec();
+ /**
+ * Return the Chimera selection specification for this object
+ *
+ * @return a String representing a Chimera atom-spec
+ */
+ public String toSpec();
- /**
- * Return a String representation for this object
- *
- * @return a String representing the object name
- */
- public String toString();
+ /**
+ * Return a String representation for this object
+ *
+ * @return a String representing the object name
+ */
+ public String toString();
- /**
- * Return the userData for this object
- *
- * @return an Object representing the userData (usually TreePath)
- */
- public Object getUserData();
+ /**
+ * Return the userData for this object
+ *
+ * @return an Object representing the userData (usually TreePath)
+ */
+ public Object getUserData();
- /**
- * Set the userData for this object
- *
- * @param userData
- * the Object representing the userData (usually TreePath)
- */
- public void setUserData(Object userData);
+ /**
+ * Set the userData for this object
+ *
+ * @param userData
+ * the Object representing the userData (usually TreePath)
+ */
+ public void setUserData(Object userData);
- /**
- * Return the ChimeraModel for this object
- *
- * @return the ChimeraModel this object is part of
- */
- public ChimeraModel getChimeraModel();
+ /**
+ * Return the ChimeraModel for this object
+ *
+ * @return the ChimeraModel this object is part of
+ */
+ public ChimeraModel getChimeraModel();
- /**
- * Set the "selected" state of this object
- *
- * @param selected
- * boolean value as to whether this object is selected
- */
- public void setSelected(boolean selected);
+ /**
+ * Set the "selected" state of this object
+ *
+ * @param selected
+ * boolean value as to whether this object is selected
+ */
+ public void setSelected(boolean selected);
- /**
- * Get the "selected" state of this object
- *
- * @return the selected state of this object
- */
- public boolean isSelected();
+ /**
+ * Get the "selected" state of this object
+ *
+ * @return the selected state of this object
+ */
+ public boolean isSelected();
- /**
- * Get the selected state of this object and its children.
- *
- * @return true if any child is selected.
- */
- public boolean hasSelectedChildren();
+ /**
+ * Get the selected state of this object and its children.
+ *
+ * @return true if any child is selected.
+ */
+ public boolean hasSelectedChildren();
- /**
- * Get the children of this object (if any)
- *
- * @return the children of the object
- */
- public List<ChimeraStructuralObject> getChildren();
+ /**
+ * Get the children of this object (if any)
+ *
+ * @return the children of the object
+ */
+ public List<ChimeraStructuralObject> getChildren();
}
// StructureViz imports
/**
- * The ChimeraTreeModel class provides the underlying model
- * for the navigation tree in the ModelNavigatorDialog.
+ * The ChimeraTreeModel class provides the underlying model for the navigation
+ * tree in the ModelNavigatorDialog.
*
* @author scooter
* @see ModelNavigatorDialog
- */
-public class ChimeraTreeModel extends DefaultTreeModel {
- private ChimeraManager chimeraManager;
- private JTree navigationTree;
- private int residueDisplay = ChimeraResidue.THREE_LETTER;
-
- /**
- * Constructor for the ChimeraTreeModel.
- *
- * @param chimeraObject the Chimera object that this tree represents
- * @param tree the JTree used to display the object
- * @see Chimera
- */
- public ChimeraTreeModel (ChimeraManager chimeraManager, JTree tree) {
- super(new DefaultMutableTreeNode());
- this.chimeraManager = chimeraManager;
- this.navigationTree = tree;
- DefaultMutableTreeNode rootNode = buildTree();
- this.setRoot(rootNode);
- }
-
- /**
- * Set the display type for the residues. The display type
- * must be one of:
- *
- * ChimeraResidue.THREE_LETTER
- * ChimeraResidue.SINGLE_LETTER
- * ChimeraResidue.FULL_NAME
- *
- * @param newDisplay the display type
- * @see ChimeraResidue
- */
- public void setResidueDisplay(int newDisplay) {
- this.residueDisplay = newDisplay;
- }
-
- /**
- * This method is called to rebuild the tree model "from scratch"
- */
- public void reload() {
- // First, rebuild the tree with the new data
- DefaultMutableTreeNode rootNode = buildTree();
- this.setRoot(rootNode);
-
- // Now let the superclass do all of the work
- super.reload();
- }
-
- /**
- * Rebuild an existing tree
- */
- public void rebuildTree() {
- DefaultMutableTreeNode rootNode = buildTree();
- DefaultTreeModel model = (DefaultTreeModel)navigationTree.getModel();
- model.setRoot(rootNode);
- model.reload();
- }
-
- /**
- * Build the tree from the current Chimera data
- *
- * @return DefaultMutableTreeNode that represents the currently loaded Chimera models
- */
- private DefaultMutableTreeNode buildTree() {
- int modelCount = chimeraManager.getChimeraModelsCount(true);
- DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount+" Open Chimera Models");
- TreePath rootPath = new TreePath(rootNode);
-
- TreePath path = null;
- DefaultMutableTreeNode model = null;
-
- // Add all of the Chimera models
- for (ChimeraModel chimeraModel: chimeraManager.getChimeraModels()) {
- model = new DefaultMutableTreeNode(chimeraModel);
- path = rootPath.pathByAddingChild(model);
- chimeraModel.setUserData(path);
- addChainNodes(chimeraModel, model, path);
- rootNode.add(model);
- }
- return rootNode;
- }
-
- /**
- * add chains to a tree model
- *
- * @param chimeraModel the ChimeraModel to get the chains from
- * @param treeModel the tree model to add the chains to
- * @param treePath the tree path where the chains should be added
- */
- private void addChainNodes(ChimeraModel chimeraModel,
- DefaultMutableTreeNode treeModel,
- TreePath treePath) {
- DefaultMutableTreeNode chain = null;
- TreePath chainPath = null;
-
- // Get the list of chains
- Collection<ChimeraChain> chainList = chimeraModel.getChains();
-
- if (chainList.size() == 0) {
- // No chains! Just add the residues
- addResidues(chimeraModel.getResidues(), treeModel, treePath);
- return;
- }
-
- // Iterate over the chains and add the chain and all of
- // the chain's residues
- for (ChimeraChain chimeraChain: chainList) {
- chain = new DefaultMutableTreeNode(chimeraChain);
- chainPath = treePath.pathByAddingChild(chain);
- chimeraChain.setUserData(chainPath);
- addResidues(chimeraChain.getResidues(), chain, chainPath);
- treeModel.add(chain);
- }
- }
-
- /**
- * add residues to a tree model
- *
- * @param residues the residues to add
- * @param treeModel the tree model to add the residues to
- * @param treePath the tree path where the residues should be added
- */
- private void addResidues(Collection<ChimeraResidue> residues,
- DefaultMutableTreeNode treeModel,
- TreePath treePath) {
- DefaultMutableTreeNode residue = null;
- TreePath residuePath = null;
-
- List<ChimeraResidue> sortedResidues = new ArrayList<ChimeraResidue>(residues);
- Collections.sort(sortedResidues);
-
- // Iterate over all residues & add them to the tree
- for (ChimeraResidue res: sortedResidues) {
- res.setDisplayType(this.residueDisplay);
- residue = new DefaultMutableTreeNode(res);
- residuePath = treePath.pathByAddingChild(residue);
- res.setUserData(residuePath);
- treeModel.add(residue);
- }
- }
+ */
+public class ChimeraTreeModel extends DefaultTreeModel
+{
+ private ChimeraManager chimeraManager;
+
+ private JTree navigationTree;
+
+ private int residueDisplay = ChimeraResidue.THREE_LETTER;
+
+ /**
+ * Constructor for the ChimeraTreeModel.
+ *
+ * @param chimeraObject
+ * the Chimera object that this tree represents
+ * @param tree
+ * the JTree used to display the object
+ * @see Chimera
+ */
+ public ChimeraTreeModel(ChimeraManager chimeraManager, JTree tree)
+ {
+ super(new DefaultMutableTreeNode());
+ this.chimeraManager = chimeraManager;
+ this.navigationTree = tree;
+ DefaultMutableTreeNode rootNode = buildTree();
+ this.setRoot(rootNode);
+ }
+
+ /**
+ * Set the display type for the residues. The display type must be one of:
+ *
+ * ChimeraResidue.THREE_LETTER ChimeraResidue.SINGLE_LETTER
+ * ChimeraResidue.FULL_NAME
+ *
+ * @param newDisplay
+ * the display type
+ * @see ChimeraResidue
+ */
+ public void setResidueDisplay(int newDisplay)
+ {
+ this.residueDisplay = newDisplay;
+ }
+
+ /**
+ * This method is called to rebuild the tree model "from scratch"
+ */
+ public void reload()
+ {
+ // First, rebuild the tree with the new data
+ DefaultMutableTreeNode rootNode = buildTree();
+ this.setRoot(rootNode);
+
+ // Now let the superclass do all of the work
+ super.reload();
+ }
+
+ /**
+ * Rebuild an existing tree
+ */
+ public void rebuildTree()
+ {
+ DefaultMutableTreeNode rootNode = buildTree();
+ DefaultTreeModel model = (DefaultTreeModel) navigationTree.getModel();
+ model.setRoot(rootNode);
+ model.reload();
+ }
+
+ /**
+ * Build the tree from the current Chimera data
+ *
+ * @return DefaultMutableTreeNode that represents the currently loaded Chimera
+ * models
+ */
+ private DefaultMutableTreeNode buildTree()
+ {
+ int modelCount = chimeraManager.getChimeraModelsCount(true);
+ DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount
+ + " Open Chimera Models");
+ TreePath rootPath = new TreePath(rootNode);
+
+ TreePath path = null;
+ DefaultMutableTreeNode model = null;
+
+ // Add all of the Chimera models
+ for (ChimeraModel chimeraModel : chimeraManager.getChimeraModels())
+ {
+ model = new DefaultMutableTreeNode(chimeraModel);
+ path = rootPath.pathByAddingChild(model);
+ chimeraModel.setUserData(path);
+ addChainNodes(chimeraModel, model, path);
+ rootNode.add(model);
+ }
+ return rootNode;
+ }
+
+ /**
+ * add chains to a tree model
+ *
+ * @param chimeraModel
+ * the ChimeraModel to get the chains from
+ * @param treeModel
+ * the tree model to add the chains to
+ * @param treePath
+ * the tree path where the chains should be added
+ */
+ private void addChainNodes(ChimeraModel chimeraModel,
+ DefaultMutableTreeNode treeModel, TreePath treePath)
+ {
+ DefaultMutableTreeNode chain = null;
+ TreePath chainPath = null;
+
+ // Get the list of chains
+ Collection<ChimeraChain> chainList = chimeraModel.getChains();
+
+ if (chainList.size() == 0)
+ {
+ // No chains! Just add the residues
+ addResidues(chimeraModel.getResidues(), treeModel, treePath);
+ return;
+ }
+
+ // Iterate over the chains and add the chain and all of
+ // the chain's residues
+ for (ChimeraChain chimeraChain : chainList)
+ {
+ chain = new DefaultMutableTreeNode(chimeraChain);
+ chainPath = treePath.pathByAddingChild(chain);
+ chimeraChain.setUserData(chainPath);
+ addResidues(chimeraChain.getResidues(), chain, chainPath);
+ treeModel.add(chain);
+ }
+ }
+
+ /**
+ * add residues to a tree model
+ *
+ * @param residues
+ * the residues to add
+ * @param treeModel
+ * the tree model to add the residues to
+ * @param treePath
+ * the tree path where the residues should be added
+ */
+ private void addResidues(Collection<ChimeraResidue> residues,
+ DefaultMutableTreeNode treeModel, TreePath treePath)
+ {
+ DefaultMutableTreeNode residue = null;
+ TreePath residuePath = null;
+
+ List<ChimeraResidue> sortedResidues = new ArrayList<ChimeraResidue>(
+ residues);
+ Collections.sort(sortedResidues);
+
+ // Iterate over all residues & add them to the tree
+ for (ChimeraResidue res : sortedResidues)
+ {
+ res.setDisplayType(this.residueDisplay);
+ residue = new DefaultMutableTreeNode(res);
+ residuePath = treePath.pathByAddingChild(residue);
+ res.setUserData(residuePath);
+ treeModel.add(residue);
+ }
+ }
}
public class StructureManager
{
- static final String[] defaultStructureKeys =
- { "Structure", "pdb", "pdbFileName", "PDB ID", "structure",
- "biopax.xref.PDB", "pdb_ids", "ModelName", "ModelNumber" };
+ static final String[] defaultStructureKeys = { "Structure", "pdb",
+ "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
+ "ModelName", "ModelNumber" };
- static final String[] defaultChemStructKeys =
- { "Smiles", "smiles", "SMILES" };
+ static final String[] defaultChemStructKeys = { "Smiles", "smiles",
+ "SMILES" };
- static final String[] defaultResidueKeys =
- { "FunctionalResidues", "ResidueList", "Residues" };
+ static final String[] defaultResidueKeys = { "FunctionalResidues",
+ "ResidueList", "Residues" };
public enum ModelType
{
package ext.edu.ucsf.rbvi.strucviz2;
/**
- * This object maintains the relationship between Chimera objects and Cytoscape objects.
+ * This object maintains the relationship between Chimera objects and Cytoscape
+ * objects.
*/
-public class StructureSettings {
+public class StructureSettings
+{
-// @Tunable(description = "Path to UCSF Chimera application", gravity = 4.0)
- public String chimeraPath = null;
+ // @Tunable(description = "Path to UCSF Chimera application", gravity = 4.0)
+ public String chimeraPath = null;
- public StructureSettings(StructureManager manager) {
-
- chimeraPath = manager.getCurrentChimeraPath(null);
+ public StructureSettings(StructureManager manager)
+ {
- // This seems a little strange, but it has to do with the order of tunable interceptor
- // handling. We need to set these selectors in our structure manager and dynamically
- // pull the data out as needed....
- manager.setStructureSettings( this);
- }
+ chimeraPath = manager.getCurrentChimeraPath(null);
+ // This seems a little strange, but it has to do with the order of tunable
+ // interceptor
+ // handling. We need to set these selectors in our structure manager and
+ // dynamically
+ // pull the data out as needed....
+ manager.setStructureSettings(this);
+ }
- public String getChimeraPath() {
- return chimeraPath;
- }
+ public String getChimeraPath()
+ {
+ return chimeraPath;
+ }
}
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+ throw new javax.xml.rpc.ServiceException(
+ MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[] { portName }));
}
}
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+ throw new javax.xml.rpc.ServiceException(
+ MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[] { portName }));
}
}
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { seq });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seq });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { msf });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { msf });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { job_id });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { job_id });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+ throw new javax.xml.rpc.ServiceException(
+ MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[] { portName }));
}
}
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { seqSet });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { seqSet });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { job_id });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { job_id });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobId });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- {});
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
if (_resp instanceof java.rmi.RemoteException)
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+ throw new javax.xml.rpc.ServiceException(
+ MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[] { portName }));
}
}
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- {});
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { job_id });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[] { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { al, database });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { al,
+ database });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { s, database });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { s,
+ database });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobId });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
if (_resp instanceof java.rmi.RemoteException)
{
if (profile)
{
// TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, nongap } });
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, nongap } });
}
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
.append("%");
}
consensus.annotations[i] = new Annotation(maxRes,
- mouseOver.toString(), ' ',
- value);
+ mouseOver.toString(), ' ', value);
}
}
* @param hashtable
* @return
*/
- public static int[] extractCdnaProfile(Hashtable hashtable, boolean ignoreGaps)
+ public static int[] extractCdnaProfile(Hashtable hashtable,
+ boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
result[1] = distinctValuesCount;
return Arrays.copyOfRange(result, 0, j);
}
-
+
/**
* Compute a consensus for the cDNA coding for a protein alignment.
*
final int pct = codonCount * 100 / totalCount;
String codon = String
.valueOf(CodingUtils.decodeCodon(codonEncoded));
- percent = fmt == null ? Integer.toString(pct) : fmt
- .form(pct);
+ percent = fmt == null ? Integer.toString(pct) : fmt.form(pct);
if (showProfileLogo || codonCount == modalCodonCount)
{
if (percent.equals(lastPercent) && j > 0)
if (samePercent.length() > 0)
{
mouseOver.append(samePercent).append(": ")
- .append(lastPercent)
- .append("% ");
+ .append(lastPercent).append("% ");
}
samePercent.setLength(0);
samePercent.append(codon);
*/
package jalview.analysis;
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.util.MapList;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
/**
*
*
private static final String NEWLINE = System.lineSeparator();
- static String[] dna =
- { "A", "C", "G", "T", "-" };
+ static String[] dna = { "A", "C", "G", "T", "-" };
// "C", "T", "A", "G", "-"};
- static String[] pep =
- { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
- "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
+ static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",
+ "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
int[][] score;
else
{
output.append("Wrong type = dna or pep only");
- throw new Error(MessageManager.formatMessage("error.unknown_type_dna_or_pep", new String[]{type2}));
+ throw new Error(MessageManager.formatMessage(
+ "error.unknown_type_dna_or_pep", new String[] { type2 }));
}
}
*/
public static List<List<? extends Object>> replaceMatchingSeqsWith(
List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
- List<SequenceI> ochains,
- AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
+ List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
+ boolean removeOldAnnots)
{
List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
List<AlignSeq> aligs = new ArrayList<AlignSeq>();
{
ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
-
+
for (SequenceI sq : ochains)
{
SequenceI bestm = null;
int bestscore = 0;
for (SequenceI msq : al.getSequences())
{
- AlignSeq aseq = doGlobalNWAlignment(msq, sq,
- dnaOrProtein);
+ AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
if (bestm == null || aseq.getMaxScore() > bestscore)
{
bestscore = aseq.getMaxScore();
sq.setName(sp.getName());
sq.setDescription(sp.getDescription());
Mapping sp2sq;
- sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+ sq.transferAnnotation(sp,
+ sp2sq = aligns.get(q).getMappingFromS1(false));
aligs.add(aligns.get(q));
int inspos = -1;
for (int ap = 0; ap < annotations.size();)
{
inspos = ap;
}
- if (removeOldAnnots) {
+ if (removeOldAnnots)
+ {
annotations.remove(ap);
- } else {
+ }
+ else
+ {
AlignmentAnnotation alan = annotations.remove(ap);
alan.liftOver(sq, sp2sq);
alan.setSequenceRef(sq);
package jalview.analysis;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
import java.util.Map;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-
public class AlignmentAnnotationUtils
{
* @return DOCUMENT ME!
*/
private static List<SequenceI> _sortByTree(SequenceNode node,
- List<SequenceI> tmp,
- List<SequenceI> seqset)
+ List<SequenceI> tmp, List<SequenceI> seqset)
{
if (node == null)
{
public static void sortByFeature(String featureLabel, String groupLabel,
int start, int stop, AlignmentI alignment, String method)
{
- sortByFeature(featureLabel == null ? null : new String[]
- { featureLabel }, groupLabel == null ? null : new String[]
- { groupLabel }, start, stop, alignment, method);
+ sortByFeature(featureLabel == null ? null
+ : new String[] { featureLabel }, groupLabel == null ? null
+ : new String[] { groupLabel }, start, stop, alignment, method);
}
private static boolean containsIgnoreCase(final String lab,
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
StringBuffer scoreLabel = new StringBuffer();
{
if (method == FEATURE_LABEL)
{
- throw new Error(MessageManager.getString("error.not_yet_implemented"));
+ throw new Error(
+ MessageManager.getString("error.not_yet_implemented"));
}
}
if (lastSortByFeatureScore == null
* @param cdnaAlignment
* @return
*/
- public static boolean mapProteinToCdna(
- final AlignmentI proteinAlignment,
+ public static boolean mapProteinToCdna(final AlignmentI proteinAlignment,
final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
if (cdnaLength != mappedLength
&& cdnaLength > 2
&& String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
- .equals(
- ResidueProperties.START))
+ .equals(ResidueProperties.START))
{
cdnaStart += 3;
cdnaLength -= 3;
{
return null;
}
- MapList map = new MapList(new int[]
- { cdnaStart, cdnaEnd }, new int[]
- { proteinStart, proteinEnd }, 3, 1);
+ MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[] {
+ proteinStart, proteinEnd }, 3, 1);
return map;
}
&& aaResidue < aaSeqChars.length; i += 3, aaResidue++)
{
String codon = String.valueOf(cdnaSeqChars, i, 3);
- final String translated = ResidueProperties.codonTranslate(
- codon);
+ final String translated = ResidueProperties.codonTranslate(codon);
/*
* allow * in protein to match untranslatable in dna
*/
{
continue;
}
- if (translated == null
- || !(aaRes == translated.charAt(0)))
+ if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
// System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
boolean preserveUnmappedGaps)
{
/*
- * Get any mappings from the source alignment to the target (dataset) sequence.
+ * Get any mappings from the source alignment to the target (dataset)
+ * sequence.
*/
// TODO there may be one AlignedCodonFrame per dataset sequence, or one with
// all mappings. Would it help to constrain this?
{
return false;
}
-
+
/*
* Locate the aligned source sequence whose dataset sequence is mapped. We
* just take the first match here (as we can't align cDNA like more than one
break;
}
}
-
+
if (alignFrom == null)
{
return false;
* @param preserveMappedGaps
*/
public static void alignSequenceAs(SequenceI alignTo,
- SequenceI alignFrom,
- AlignedCodonFrame mapping, String myGap, char sourceGap,
- boolean preserveMappedGaps, boolean preserveUnmappedGaps)
+ SequenceI alignFrom, AlignedCodonFrame mapping, String myGap,
+ char sourceGap, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
{
// TODO generalise to work for Protein-Protein, dna-dna, dna-protein
final char[] thisSeq = alignTo.getSequence();
final char[] thatAligned = alignFrom.getSequence();
StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
-
+
// aligned and dataset sequence positions, all base zero
int thisSeqPos = 0;
int sourceDsPos = 0;
*/
protected static int calculateGapsToInsert(boolean preserveMappedGaps,
boolean preserveUnmappedGaps, int sourceGapMappedLength,
- boolean inExon, int trailingGapLength,
- int intronLength, final boolean startOfCodon)
+ boolean inExon, int trailingGapLength, int intronLength,
+ final boolean startOfCodon)
{
int gapsToAdd = 0;
if (startOfCodon)
// mapping is from protein to nucleotide
toDna = true;
// should ideally get gap count ratio from mapping
- gap = String.valueOf(new char[]
- { gapCharacter, gapCharacter, gapCharacter });
+ gap = String.valueOf(new char[] { gapCharacter, gapCharacter,
+ gapCharacter });
}
else
{
int column = 0;
for (AlignedCodon codon : alignedCodons.keySet())
{
- final Map<SequenceI, String> columnResidues = alignedCodons.get(codon);
- for (Entry<SequenceI, String> entry : columnResidues
- .entrySet())
+ final Map<SequenceI, String> columnResidues = alignedCodons
+ .get(codon);
+ for (Entry<SequenceI, String> entry : columnResidues.entrySet())
{
// place translated codon at its column position in sequence
entry.getKey().getSequence()[column] = entry.getValue().charAt(0);
* the map we are building up
*/
static void addCodonPositions(SequenceI dna, SequenceI protein,
- char gapChar,
- Mapping seqMap,
+ char gapChar, Mapping seqMap,
Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
{
Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
* @return
*/
protected static boolean isMappable(SequenceI dnaSeq,
- SequenceI proteinSeq,
- Set<AlignedCodonFrame> mappings)
+ SequenceI proteinSeq, Set<AlignedCodonFrame> mappings)
{
if (dnaSeq == null || proteinSeq == null)
{
return false;
}
- SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
+ SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq
+ .getDatasetSequence();
SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
: proteinSeq.getDatasetSequence();
-
+
/*
* Already mapped?
*/
- for (AlignedCodonFrame mapping : mappings) {
- if ( proteinDs == mapping.getAaForDnaSeq(dnaDs)) {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (proteinDs == mapping.getAaForDnaSeq(dnaDs))
+ {
return true;
}
}
* the alignment to check for presence of annotations
*/
public static void findAddableReferenceAnnotations(
- List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
+ List<SequenceI> sequenceScope,
+ Map<String, String> labelForCalcId,
final Map<SequenceI, List<AlignmentAnnotation>> candidates,
AlignmentI al)
{
{
return;
}
-
+
/*
* For each sequence in scope, make a list of any annotations on the
* underlying dataset sequence which are not already on the alignment.
* sequence.
*/
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
- .findAnnotations(seq, dsann.getCalcId(),
- dsann.label);
+ .findAnnotations(seq, dsann.getCalcId(), dsann.label);
if (!matchedAlignmentAnnotations.iterator().hasNext())
{
result.add(dsann);
endRes = selectionGroup.getEndRes();
}
copyAnn.restrict(startRes, endRes);
-
+
/*
* Add to the sequence (sets copyAnn.datasetSequence), unless the
* original annotation is already on the sequence.
Collection<String> types, List<SequenceI> forSequences,
boolean anyType, boolean doShow)
{
- for (AlignmentAnnotation aa : al
- .getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
{
if (anyType || types.contains(aa.label))
{
{
Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
List<SequenceI> exonSequences = new ArrayList<SequenceI>();
-
+
for (SequenceI dnaSeq : dna)
{
final SequenceI ds = dnaSeq.getDatasetSequence();
* contiguous exons
*/
List<int[]> exonRange = new ArrayList<int[]>();
- exonRange.add(new int[]
- { 1, newSequence.length() });
+ exonRange.add(new int[] { 1, newSequence.length() });
MapList map = new MapList(exonRange, seqMapping.getMap()
- .getToRanges(),
- 3, 1);
+ .getToRanges(), 3, 1);
newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
return description;
}
- public static SequenceAnnotationOrder forDescription(String d) {
+ public static SequenceAnnotationOrder forDescription(String d)
+ {
for (SequenceAnnotationOrder order : values())
{
if (order.toString().equals(d))
AlignmentAnnotation[] alignmentAnnotations)
{
sequenceIndices.clear();
- for (AlignmentAnnotation ann : alignmentAnnotations) {
+ for (AlignmentAnnotation ann : alignmentAnnotations)
+ {
SequenceI seq = ann.sequenceRef;
- if (seq != null) {
+ if (seq != null)
+ {
int index = AlignmentUtils.getSequenceIndex(alignment, seq);
sequenceIndices.put(seq, index);
}
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals(ht
- .get(res)) == false)
+ else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
}
{
consString.append('-');
}
- consSymbs = new String[end-start+1];
+ consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
pgaps = ((float) totGaps * 100) / sequences.length;
- consSymbs[i-start]=new String();
-
+ consSymbs[i - start] = new String();
+
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
{
if (result.intValue() == 1)
{
- consSymbs[i-start] = type+" "+consSymbs[i-start];
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
{
if (result.intValue() != -1)
{
- {
- if (result.intValue()==0) {
- consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
- } else {
- consSymbs[i-start] = type+" "+consSymbs[i-start];
- }
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
}
-
+
count++;
}
}
String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
: "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
- conssym, ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
// Quality calc
if (quality2 != null)
*/
package jalview.analysis;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.ws.SequenceFetcher;
import jalview.ws.seqfetcher.ASequenceFetcher;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
/**
* Functions for cross-referencing sequence databases. user must first specify
* if cross-referencing from protein or dna (set dna==true)
{
found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
if (found)
- {
+ {
xrfs[r] = null; // we've recovered seqs for this one.
}
}
*/
private static boolean searchDatasetXrefs(SequenceI sequenceI,
boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
- List<SequenceI> rseqs,
- AlignedCodonFrame cf)
+ List<SequenceI> rseqs, AlignedCodonFrame cf)
{
boolean found = false;
if (lrfs == null)
for (int gd = 0; gd < selection.length; gd++)
{
SequenceI dna = selection[gd];
- DBRefEntry[] dnarefs = DBRefUtils
- .selectRefs(dna.getDBRef(),
- jalview.datamodel.DBRefSource.DNACODINGDBS);
+ DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+ jalview.datamodel.DBRefSource.DNACODINGDBS);
if (dnarefs != null)
{
// intersect with pep
aa.graphHeight = annotation.graphHeight;
if (annotation.getThreshold() != null)
{
- aa.setThreshold(new GraphLine(annotation
- .getThreshold()));
+ aa.setThreshold(new GraphLine(annotation.getThreshold()));
}
if (annotation.hasScore)
{
aa = gapString;
if (skipint == null)
{
- skipint = new int[]
- { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
+ skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
+ * cdp[0],
+ * cdp[2]
+ */};
}
skipint[1] = alignedCodon.pos3; // cdp[2];
}
* range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
* iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
*/
- MapList map = new MapList(scontigs, new int[]
- { 1, resSize }, 3, 1);
+ MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
transferCodedFeatures(selection, newseq, map, null, null);
* @param proteinSeqs
* @return
*/
- protected void insertAAGap(int pos,
- List<SequenceI> proteinSeqs)
+ protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
{
aaWidth++;
for (SequenceI seq : proteinSeqs)
{
continue;
}
-// if invalid string used, then regex has no matched to/from
+ // if invalid string used, then regex has no matched to/from
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
i = 0;
for (String key : gps.keySet())
{
- SequenceGroup group = new SequenceGroup(gps.get(key),
- "Subseq: " + key, null, true, true, false, 0, width - 1);
+ SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+ + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
}
+ ((SequenceI) node.element()).getName());
}
- System.out.println(" dist = " + node.dist + " "
- + node.count + " "
+ System.out.println(" dist = " + node.dist + " " + node.count + " "
+ node.height);
}
*/
package jalview.analysis;
-import java.io.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.BinarySequence;
import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
-import jalview.math.*;
+import jalview.math.Matrix;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ScoreMatrix;
+import java.io.PrintStream;
+
/**
* Performs Principal Component Analysis on given sequences
*
*/
package jalview.analysis;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import com.stevesoft.pat.Regex;
+
public class ParseProperties
{
/**
public int getScoresFromDescription(String ScoreName,
String ScoreDescriptions, String regex, boolean repeat)
{
- return getScoresFromDescription(new String[]
- { ScoreName }, new String[]
- { ScoreDescriptions }, regex, repeat);
+ return getScoresFromDescription(new String[] { ScoreName },
+ new String[] { ScoreDescriptions }, regex, repeat);
}
public int getScoresFromDescription(String[] ScoreNames,
static Hashtable<Integer, Integer> pairHash = new Hashtable();
- private static final Character[] openingPars =
- { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J',
- 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
- 'Y', 'Z' };
+ private static final Character[] openingPars = { '(', '[', '{', '<', 'A',
+ 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O',
+ 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z' };
- private static final Character[] closingPars =
- { ')', ']', '}', '>', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j',
- 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x',
- 'y', 'z' };
+ private static final Character[] closingPars = { ')', ']', '}', '>', 'a',
+ 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o',
+ 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z' };
private static HashSet<Character> openingParsSet = new HashSet<Character>(
Arrays.asList(openingPars));
{
if (!isClosingParenthesis(closingParenthesis))
{
- throw new WUSSParseException(MessageManager.formatMessage("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", new String[]{new StringBuffer(closingParenthesis).toString()}), -1);
+ throw new WUSSParseException(
+ MessageManager.formatMessage(
+ "exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis",
+ new String[] { new StringBuffer(closingParenthesis)
+ .toString() }), -1);
}
return closingToOpening.get(closingParenthesis);
if (!stacks.containsKey(opening))
{
- throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_unseen_closing_char", new String[]{new StringBuffer(base).toString()}), i);
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_unseen_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
}
Stack<Integer> stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
- throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_closing_char", new String[]{new StringBuffer(base).toString()}), i);
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
}
int temp = stack.pop();
Stack<Integer> stack = stacks.get(opening);
if (!stack.empty())
{
- throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_opening_char", new String[]{new StringBuffer(opening).toString(),Integer.valueOf(stack.pop()).toString()}), i);
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_opening_char",
+ new String[] { new StringBuffer(opening).toString(),
+ Integer.valueOf(stack.pop()).toString() }), i);
}
}
return pairs;
*/
package jalview.analysis;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class SeqsetUtils
{
}
}
sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId", (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
- : new Vector<PDBEntry>());
+ sqinfo.put("PdbId",
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector<PDBEntry>());
sqinfo.put("datasetSequence",
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
// associated with this key.
names.put(new SeqIdName(seq.getDisplayId(true)), seq);
SequenceI dbseq = seq;
- while (dbseq.getDatasetSequence()!=null)
+ while (dbseq.getDatasetSequence() != null)
{
dbseq = dbseq.getDatasetSequence();
}
SeqIdName nam = new SeqIdName(seqnam);
List<SequenceI> m = findAllIdMatches(nam);
- if (m!=null)
+ if (m != null)
{
return m.toArray(new SequenceI[m.size()]);
}
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
}
if (profile)
{
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
{
for (int d = 65; d < 90; d++)
{
- ca[x] = new int[]
- { c, d };
+ ca[x] = new int[] { c, d };
vl[x] = pairs[c][d];
x++;
}
{
tval = (vl[c] * 100f / divisor);
mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
- + (char) ca[c][1] + " " + fmt.form(tval)
- + "%";
+ + (char) ca[c][1] + " " + fmt.form(tval) + "%";
p++;
}
{
for (int d = 65; d < 90; d++)
{
- ca[x] = new int[]
- { c, d };
+ ca[x] = new int[] { c, d };
vl[x] = pairs[c][d];
x++;
}
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.AlignmentView;
-import jalview.schemes.ScoreMatrix;
import jalview.util.Comparison;
public abstract class PairwiseSeqScoreModel implements ScoreModelI
void addHistoryItem(CommandI command);
void setShowSeqFeatures(boolean show);
-
+
void setMenusForViewport();
-
+
void changeColour(ColourSchemeI cs);
/**
boolean extendCurrent, boolean clearColumns, String featureType);
/**
- * sort the alignment or current selection by average score over the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by average score over the given set
+ * of features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
void sortAlignmentByFeatureScore(String[] typ);
/**
- * sort the alignment or current selection by distribution of the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by distribution of the given set of
+ * features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
void sortAlignmentByFeatureDensity(String[] typ);
*/
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
-
+
void setSequenceColour(SequenceI seq, Color col);
Color getSequenceColour(SequenceI seq);
/**
* get a copy of the currently visible alignment annotation
- * @param selectedOnly if true - trim to selected regions on the alignment
- * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+ *
+ * @param selectedOnly
+ * if true - trim to selected regions on the alignment
+ * @return an empty list or new alignment annotation objects shown only
+ * visible columns trimmed to selected region only
*/
List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly);
FeatureRenderer getFeatureRenderer();
FeatureRenderer cloneFeatureRenderer();
-
+
/**
*
* @return displayed name for the view
*
* @return
*/
- Map<String,Object> getFeatureColours();
+ Map<String, Object> getFeatureColours();
/**
* query the alignment view to find all features
*
* @return
*/
- Map<String,Object> getDisplayedFeatureCols();
+ Map<String, Object> getDisplayedFeatureCols();
/**
* get all registered groups
{
void discoverAllFeatureData();
-
+
}
void setUpperCasebold(boolean upperCasebold);
boolean isUpperCasebold();
-
+
boolean sameStyle(ViewStyleI them);
void setFontName(String name);
package jalview.api.analysis;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
public interface ViewBasedAnalysisI
/**
* Parameterise the analysis model using the current view
+ *
* @param view
* @return true if model is applicable and calculation should proceed
*/
* if true, force close any linked external viewer process
*/
void closeViewer(boolean closeExternalViewer);
+
/**
* apply a colourscheme to the structures in the viewer
+ *
* @param colourScheme
*/
void setJalviewColourScheme(ColourSchemeI colourScheme);
MessageManager.getString("label.sequence_details"));
MenuItem makeReferenceSeq = new MenuItem();
-
+
SequenceI seq;
MenuItem revealAll = new MenuItem();
if (sg != null && sg.getSize() > 0)
{
editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new Object[]
- { sg.getName() }));
+ "label.name_param", new Object[] { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- { target });
+ seq.getDBRef(), new String[] { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
.getString("action.set_as_reference")); // );
}
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { seq.getName() }));
+ "label.represent_group_with", new Object[] { seq.getName() }));
}
else
{
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.setShowSequenceFeatures(true);;
+ ap.av.setShowSequenceFeatures(true);
+ ;
ap.highlightSearchResults(null);
}
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.selection_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
protected void showSequenceDetails()
{
- createSequenceDetailsReport(new SequenceI[]
- { seq });
+ createSequenceDetailsReport(new SequenceI[] { seq });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid", new Object[]
- { seq.getDisplayId(true) }));
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
- : null);
+ "label.annotation_for_displayid",
+ new Object[] { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+ .getMinMax() : null);
contents.append("</p>");
}
Frame frame = new Frame();
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
cap.setText(MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() }));
+ new Object[] { contents.toString() }));
}
void editName()
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+ null, ap, AppletFormatAdapter.URL);
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, AppletFormatAdapter.URL);
}
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence", new Object[]
- { seq.getName() }), 400, 300);
+ "label.paste_pdb_file_for_sequence",
+ new Object[] { seq.getName() }), 400, 300);
}
}
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { "" }));
+ "label.represent_group_with", new Object[] { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
menu1.setLabel(MessageManager.getString("label.group") + ":");
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
+ clustalColour.setLabel(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(this);
zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_percentage"));
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(MessageManager
.getString("label.percentage_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setLabel(MessageManager
+ .getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
getGroup().setDisplayText(showText.getState());
refresh();
}
+
public void makeReferenceSeq_actionPerformed()
{
if (!ap.av.getAlignment().hasSeqrep())
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null || sg.getSize() < 1)
{
- ap.av.hideSequence(new SequenceI[]
- { seq });
+ ap.av.hideSequence(new SequenceI[] { seq });
return;
}
{
showMenu.removeAll();
hideMenu.removeAll();
-
+
final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
hideMenu.addSeparator();
-
+
final AlignmentAnnotation[] annotations = ap.getAlignment()
.getAlignmentAnnotation();
-
+
/*
* Find shown/hidden annotations types, distinguished by source (calcId),
* and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
*/
Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
- AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
- hiddenTypes,
- AlignmentAnnotationUtils.asList(annotations),
- forSequences);
-
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
for (String calcId : hiddenTypes.keySet())
{
for (List<String> type : hiddenTypes.get(calcId))
{
- addAnnotationTypeToShowHide(showMenu, forSequences,
- calcId, type, false, true);
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
}
}
// grey out 'show annotations' if none are hidden
showMenu.setEnabled(!hiddenTypes.isEmpty());
-
+
for (String calcId : shownTypes.keySet())
{
for (List<String> type : shownTypes.get(calcId))
{
- addAnnotationTypeToShowHide(hideMenu, forSequences,
- calcId, type, false, false);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
}
}
// grey out 'hide annotations' if none are shown
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
- forSequences, allTypes, actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
refresh();
}
});
* @param title
* @param embedded
*/
- public AlignFrame(AlignmentI al, JalviewLite applet,
- String title, boolean embedded)
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded)
{
this(al, applet, title, embedded, true);
}
* @param embedded
* @param addToDisplay
*/
- public AlignFrame(AlignmentI al, JalviewLite applet,
- String title, boolean embedded, boolean addToDisplay)
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
{
this(al, null, null, applet, title, embedded, addToDisplay);
}
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type)
- .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().getFeatureColours(), featureLinks,
- true, viewport.applet.getDefaultParameter(
- "relaxedidmatch", false));
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
+ .getAlignment(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours(), featureLinks,
+ true, viewport.applet.getDefaultParameter("relaxedidmatch",
+ false));
} catch (Exception ex)
{
ex.printStackTrace();
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode", new String[]
- { (viewport.cursorMode ? "on" : "off") }));
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
{
boolean visible = (aa.sequenceRef == null ? showForAlignment
: showForSequences);
- aa.visible = visible;
+ aa.visible = visible;
}
alignPanel.validateAnnotationDimensions(true);
validate();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new String[]
- { getTitle() }), 400, 250);
+ "label.alignment_properties", new String[] { getTitle() }),
+ 400, 250);
}
else if (source == overviewMenuItem)
{
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
return annotation;
}
- private Map<String,Object> getDisplayedFeatureCols()
+ private Map<String, Object> getDisplayedFeatureCols()
{
if (alignPanel.getFeatureRenderer() != null
- && viewport.getFeaturesDisplayed()!= null)
+ && viewport.getFeaturesDisplayed() != null)
{
return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
-
+
}
return null;
}
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setLabel(MessageManager.formatMessage(
- "label.undo_command", new Object[]
- { command.getDescription() }));
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
}
else
{
CommandI command = viewport.getRedoList().peek();
redoMenuItem.setLabel(MessageManager.formatMessage(
- "label.redo_command", new Object[]
- { command.getDescription() }));
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
}
else
{
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ copiedHiddenColumns.addElement(new int[] {
+ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
if (newAlignment)
{
- String newtitle = MessageManager.getString("label.copied_sequences");
- if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
+ String newtitle = MessageManager
+ .getString("label.copied_sequences");
+ if (getTitle().startsWith(
+ MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
+ newtitle = newtitle.concat(MessageManager.formatMessage(
+ "label.from_msname", new String[] { getTitle() }));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns", new String[]
- { Integer.valueOf(trimRegion.getSize()).toString() }));
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns", new String[]
- { Integer.valueOf(removeGapCols.getSize()).toString() }));
+ "label.removed_empty_columns",
+ new String[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
// This is to maintain viewport position on first residue
// of first sequence
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
-
+
fr.setGroupVisibility(Arrays.asList(groups), state);
alignPanel.seqPanel.seqCanvas.repaint();
if (alignPanel.overviewPanel != null)
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new String[]
- { this.getTitle() }), overview.getPreferredSize().width,
+ "label.overview_params", new String[] { this.getTitle() }),
+ overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
addHistoryItem(new OrderCommand(MessageManager.formatMessage(
- "label.order_by_params", new String[]
- { title }), oldOrder, viewport.getAlignment()));
+ "label.order_by_params", new String[] { title }), oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString(MessageManager.formatMessage(
- "label.jalviewLite_release", new String[]
- { version }), x, y += fh);
+ "label.jalviewLite_release", new String[] { version }), x,
+ y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
g.drawString(MessageManager.formatMessage(
- "label.jaview_build_date", new String[]
- { builddate }), x, y += fh);
+ "label.jaview_build_date", new String[] { builddate }), x,
+ y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g.drawString(MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
- jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
- frameWidth,
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
frameHeight);
}
}
// TODO: search for a jmv that involves viewer
if (jmv == null)
{ // create a new viewer/jalview binding.
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
- { seqs });
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
}
return jmv;
{
if (seqs[i] != null)
{
- sequences.addElement(new Object[]
- { seqs[i], (chains != null) ? chains[i] : null });
+ sequences.addElement(new Object[] { seqs[i],
+ (chains != null) ? chains[i] : null });
}
}
seqs = new SequenceI[sequences.size()];
chains[i] = (String) oj[1];
}
}
- return new Object[]
- { seqs, chains };
+ return new Object[] { seqs, chains };
}
this.splitFrame = sf;
}
- // may not need this
+ // may not need this
@Override
public void setShowSeqFeatures(boolean b)
{
// setMenusFromViewport(viewport);
}
+
@Override
public void refreshFeatureUI(boolean enableIfNecessary)
{
return font;
}
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
return currentTree;
}
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
public void sendSelection()
{
getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
/**
}
}
-
}
{
return av;
}
+
public SequenceRenderer getSequenceRenderer()
{
return seqPanel.seqCanvas.sr;
}
+
@Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.fr;
}
+
@Override
public jalview.api.FeatureRenderer cloneFeatureRenderer()
{
nfr.transferSettings(seqPanel.seqCanvas.fr);
return nfr;
}
+
public void alignmentChanged()
{
av.alignmentChanged(this);
// setScrollValues(start, seqIndex);
// }
// logic copied from jalview.gui.AlignmentPanel:
- if ((startv = av.getStartRes()) >= start)
- {
- /*
- * Scroll left to make start of search results visible
- */
- setScrollValues(start - 1, seqIndex);
- }
- else if ((endv = av.getEndRes()) <= end)
- {
- /*
- * Scroll right to make end of search results visible
- */
- setScrollValues(startv + 1 + end - endv, seqIndex);
- }
- else if ((starts = av.getStartSeq()) > seqIndex)
- {
- /*
- * Scroll up to make start of search results visible
- */
- setScrollValues(av.getStartRes(), seqIndex);
- }
- else if ((ends = av.getEndSeq()) <= seqIndex)
- {
- /*
- * Scroll down to make end of search results visible
- */
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
- }
+ if ((startv = av.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
+ {
/*
- * Else results are already visible - no need to scroll
+ * Scroll up to make start of search results visible
*/
+ setScrollValues(av.getStartRes(), seqIndex);
+ }
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
updateView();
}
- public class FurtherActionPanel extends Panel implements
- ItemListener
+ public class FurtherActionPanel extends Panel implements ItemListener
{
private AnnotationColumnChooser aColChooser;
*/
package jalview.appletgui;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
import java.awt.Checkbox;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
import java.util.Collections;
import java.util.Vector;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
{
if (aaa.groupRef != null)
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
+ MessageManager
+ .getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
popup.add(cprofl);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager
+ .getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
else
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
});
popup.add(chist);
final CheckboxMenuItem cprof = new CheckboxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
});
popup.add(cprof);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(Arrays
+ .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- // we make a copy rather than edit the current selection if no modifiers pressed
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
- } else {
+ }
+ else
+ {
if (evt.isControlDown())
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
- } else {
- // notionally, we should also add intermediate sequences from last added sequence ?
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
sg.addSequence(aa[selectedRow].sequenceRef, true);
}
}
- } else {
+ }
+ else
+ {
sg = new SequenceGroup();
sg.setStartRes(0);
- sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns
- .addElement(new int[]
- { region[0], region[1] });
+ .addElement(new int[] { region[0], region[1] });
}
}
}
import java.awt.event.ActionEvent;
import java.util.Vector;
-
-
@SuppressWarnings("serial")
public abstract class AnnotationRowFilter extends Panel
{
*/
protected boolean sliderDragging = false;
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
}
-
public Vector getAnnotationItems(boolean isSeqAssociated)
{
Vector list = new Vector();
}
}
-
protected void populateThresholdComboBox(Choice threshold)
{
threshold.addItem(MessageManager
.getString("label.threshold_feature_below_thereshold"));
}
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+ new String[][] { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
}
if (freader == null)
{
- throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
// TODO: JAL-1102 - should have a warning message in dialog, not simply
// overwrite the broken input data with the exception
textarea.setText(MessageManager.formatMessage(
- "label.could_not_parse_newick_file", new Object[]
- { ex.getMessage() }));
+ "label.could_not_parse_newick_file",
+ new Object[] { ex.getMessage() }));
return false;
}
return false;
*/
protected boolean openSplitFrame(AlignmentI al, String format)
{
- final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+ final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+ .getAlignment();
if (thisAlignment.isNucleotide() == al.isNucleotide())
{
// both nucleotide or both protein
dialog.setMainPanel(question);
dialog.setVisible(true);
dialog.toFront();
-
+
if (!dialog.accept)
{
return false;
AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
"Cut & Paste input - " + format, false, false);
AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
- AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
- : newFrame;
+ AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
sf.addToDisplay(false, applet);
return true;
jalview.io.AppletFormatAdapter.PASTE);
if (tcf.isValid())
{
- if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
- true))
+ if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
{
alignFrame.tcoffeeColour.setEnabled(true);
alignFrame.alignPanel.fontChanged();
// file valid but didn't get added to alignment for some reason
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.failed_add_tcoffee_scores",
- new Object[]
- { (tcf.getWarningMessage() != null ? tcf
+ new Object[] { (tcf.getWarningMessage() != null ? tcf
.getWarningMessage() : "") }));
}
}
if (tcf == null)
{
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
+ textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
if (alignFrame.alignPanel.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
else
{
- new MCview.AppletPDBViewer(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
}
*/
package jalview.appletgui;
-import java.awt.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.TextField;
public class EditNameDialog extends JVDialog
{
*/
public class EmbmenuFrame extends Frame implements MouseListener
{
- protected static final Font FONT_ARIAL_PLAIN_11 = new Font(
- "Arial", Font.PLAIN, 11);
+ protected static final Font FONT_ARIAL_PLAIN_11 = new Font("Arial",
+ Font.PLAIN, 11);
public static final Font DEFAULT_MENU_FONT = FONT_ARIAL_PLAIN_11;
* @return the panel instance for convenience.
*/
protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, Font font,
- boolean overrideFonts,
- Panel embeddedMenu,
+ boolean overrideFonts, Panel embeddedMenu,
MouseListener clickHandler)
{
if (overrideFonts)
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+
public class FeatureColourChooser extends Panel implements ActionListener,
AdjustmentListener, ItemListener, MouseListener
{
slider.addMouseListener(this);
owner = (af != null) ? af : fs.frame;
frame = new JVDialog(owner, MessageManager.formatMessage(
- "label.graduated_color_for_params", new String[]
- { type }), true, 480, 248);
+ "label.graduated_color_for_params", new String[] { type }),
+ true, 480, 248);
frame.setMainPanel(this);
validate();
frame.setVisible(true);
*/
package jalview.appletgui;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Choice;
import java.awt.event.ActionListener;
import java.util.Hashtable;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
/**
* DOCUMENT ME!
*
String title = newFeatures ? MessageManager
.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[]
- { sequences[0].getName() });
+ new String[] { sequences[0].getName() });
final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
240);
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
scrollPane.add(featurePanel);
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
add(scrollPane, BorderLayout.CENTER);
}
if (groupPanel != null)
{
- groupPanel
- .setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1,
- 4)); // JBPNote - this was scaled on number of visible groups. seems broken
+ groupPanel.setLayout(new GridLayout(
+ (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+ // scaled on number of
+ // visible groups. seems
+ // broken
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
int width = 300;
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.sequence_feature_settings"),
- width,
- height);
+ width, height);
}
public void paint(Graphics g)
final String type = check.type;
final Object typeCol = fr.getFeatureStyle(type);
java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
- "label.settings_for_type", new String[]
- { type }));
+ "label.settings_for_type", new String[] { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(new String[] { type });
}
});
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(new String[] { type });
}
});
@Override
public void discoverAllFeatureData()
{
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
rebuildGroups();
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- for (String group:fr.getFeatureGroups())
+ for (String group : fr.getFeatureGroups())
{
boolean vis = fr.checkGroupVisibility(group, false);
Checkbox check = new MyCheckbox(group, vis,
groupPanel.validate();
}
}
+
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
selectionChanged();
}
- private ItemListener groupItemListener = new ItemListener() {
- public void itemStateChanged(ItemEvent evt) {
+ private ItemListener groupItemListener = new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
Checkbox source = (Checkbox) evt.getSource();
- fr.setGroupVisibility(source.getLabel(),
- source.getState());
+ fr.setGroupVisibility(source.getLabel(), source.getState());
ap.seqPanel.seqCanvas.repaint();
if (ap.overviewPanel != null)
{
return;
};
};
+
public void itemStateChanged(ItemEvent evt)
{
selectionChanged();
}
else
{
- throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_unsupported_feature_colour_object"));
}
refreshTable();
}
}
else
{
- throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
message += searchResults.getSize() + " subsequence matches.";
}
ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.search_results", new String[]
- { searchString, message }));
+ "label.search_results", new String[] { searchString,
+ message }));
}
else
{
// TODO: indicate sequence and matching position in status bar
ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.found_match_for", new String[]
- { searchString }));
+ "label.found_match_for", new String[] { searchString }));
}
}
}
*/
package jalview.appletgui;
+import jalview.api.ViewStyleI;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Checkbox;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-import jalview.api.ViewStyleI;
-import jalview.util.MessageManager;
-
/**
* This dialog allows the user to try different font settings and related
* options. Changes are immediately visible on the alignment or tree. The user
}
public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
- int i, int starty,
- int ypos)
+ int i, int starty, int ypos)
{
int charHeight = av.getCharHeight();
* local copy of av.getCharHeight set at top of drawIds
*/
private int avcharHeight;
+
void drawIds(int starty, int endy)
{
// hardwired italic IDs in applet currently
gg.setColor(Color.blue);
if (below)
{
- gg.fillPolygon(new int[]
- { getSize().width - avcharHeight, getSize().width - avcharHeight,
- getSize().width }, new int[]
- { (i - starty) * avcharHeight + yoffset,
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty) * avcharHeight + yoffset,
(i - starty) * avcharHeight + yoffset + avcharHeight / 4,
(i - starty) * avcharHeight + yoffset }, 3);
}
if (above)
{
- gg.fillPolygon(new int[]
- { getSize().width - avcharHeight, getSize().width - avcharHeight,
- getSize().width }, new int[]
- { (i - starty + 1) * avcharHeight + yoffset,
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty + 1) * avcharHeight + yoffset,
(i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
(i - starty + 1) * avcharHeight + yoffset }, 3);
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
public class JVDialog extends Dialog implements ActionListener
{
}
if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = color.darker().darker();
}
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
public class PCAPanel extends EmbmenuFrame implements Runnable,
ActionListener, ItemListener
{
*/
package jalview.appletgui;
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Component;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
}
}
- EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
Action.CUT, deleted, 0, width, ap.av.getAlignment());
AlignmentI alignment = ap.av.getAlignment();
for (int i = 0; i < del.size(); i++)
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
{
ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
ap.paintAlignment(true);
*/
package jalview.appletgui;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.util.Format;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
public class RotatableCanvas extends Panel implements MouseListener,
MouseMotionListener, KeyListener, RotatableCanvasI
{
maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
}
- gg.drawLine(
-((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
+ gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
y + 2,
- ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- y + (fm.getDescent() * 2));
+ ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+ + (fm.getDescent() * 2));
}
else
{
- gg.drawLine(
-((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- y + fm.getDescent(),
- ((i - startx - 1) * avcharWidth)
- + (avcharWidth / 2),
- y + (fm.getDescent() * 2));
+ gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+ + fm.getDescent(), ((i - startx - 1) * avcharWidth)
+ + (avcharWidth / 2), y + (fm.getDescent() * 2));
}
}
continue;
}
- gg.fillPolygon(new int[]
- { res * avcharWidth - avcharHeight / 4,
+ gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
res * avcharWidth + avcharHeight / 4, res * avcharWidth },
- new int[]
- { y - avcharHeight / 2, y - avcharHeight / 2, y + 8 },
- 3);
+ new int[] { y - avcharHeight / 2, y - avcharHeight / 2,
+ y + 8 }, 3);
}
}
continue;
}
- gg.fillPolygon(new int[]
- { res * avcharWidth - avcharHeight / 4,
+ gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
res * avcharWidth + avcharHeight / 4, res * avcharWidth },
- new int[]
- { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+ new int[] { ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2),
ypos - (avcharHeight / 2) + 8 }, 3);
}
}
private void drawPanel(Graphics g1, int startRes, int endRes,
- int startSeq,
- int endSeq, int offset)
+ int startSeq, int endSeq, int offset)
{
-
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
break;
}
- group = av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}
}
if (features != null && features.length > 0)
{
- seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features, false, ap);
+ seqCanvas.getFeatureRenderer().amendFeatures(
+ new SequenceI[] { sequence }, features, false, ap);
seqCanvas.highlightSearchResults(null);
}
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
y -= hgap;
}
else
{
- obj = "X".equalsIgnoreCase(ch) ? "X"
- : ResidueProperties.aa2Triplet.get(ch);
+ obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
+ .get(ch);
if (obj != null)
{
text.append(" Residue: ").append(obj);
for (int i = 0; i < features.length; i++)
{
if (av.getFeaturesDisplayed() == null
- || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
+ || !av.getFeaturesDisplayed().isVisible(
+ features[i].getType()))
{
continue;
}
if (features[i].featureGroup != null
- && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
+ && !seqCanvas.fr.checkGroupVisibility(
+ features[i].featureGroup, false))
{
continue;
}
if (editCommand == null)
{
editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[]
- { label }));
+ "label.edit_params", new String[] { label }));
}
}
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP,
+ new SequenceI[] { seq }, lastres, startres - lastres,
+ av.getAlignment(), true);
}
}
else
endEditing();
break;
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
}
}
else
if (max > 0)
{
- editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.getAlignment(), true);
+ editCommand.appendEdit(Action.DELETE_GAP,
+ new SequenceI[] { seq }, startres, max,
+ av.getAlignment(), true);
}
}
}
protected boolean selectionFromTranslation(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
- if (!(source instanceof AlignViewportI)) {
+ if (!(source instanceof AlignViewportI))
+ {
return false;
}
final AlignViewportI sourceAv = (AlignViewportI) source;
- if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
{
return false;
}
-
+
/*
* Map sequence selection
*/
SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
av.setSelectionGroup(sg);
av.isSelectionGroupChanged(true);
-
+
/*
* Map column selection
*/
av);
av.setColumnSelection(cs);
av.isColSelChanged(true);
-
+
ap.scalePanelHolder.repaint();
ap.repaint();
-
+
return true;
}
}
if (currentSequenceGroup.getShowNonconserved())
{
- s = getDisplayChar(srep, i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.');
}
}
else
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.');
}
}
}
- private char getDisplayChar(final boolean usesrep, int position,
- char s, char c)
+ private char getDisplayChar(final boolean usesrep, int position, char s,
+ char c)
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep()
+ .getCharAt(position)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
{
s = c;
sp.cs = cs;
}
- conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
+ conservationSlider
+ .setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
{
sp.setAllGroupsCheckEnabled(true);
pid = (SliderPanel) PIDSlider.getComponent(0);
pid.cs = cs;
}
- PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+ PIDSlider.setTitle(MessageManager
+ .formatMessage("label.percentage_identity_thereshold",
+ new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
{
package jalview.appletgui;
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.structure.StructureSelectionManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
public class SplitFrame extends EmbmenuFrame
{
private static final long serialVersionUID = 1L;
*/
package jalview.appletgui;
-import java.applet.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import java.applet.Applet;
+import java.awt.Canvas;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.LayoutManager;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.StringTokenizer;
public class Tooltip extends Canvas implements MouseListener,
MouseMotionListener
*/
package jalview.appletgui;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
import java.awt.Button;
import java.awt.Color;
import java.awt.Component;
import java.awt.event.MouseEvent;
import java.util.Vector;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.MessageManager;
-
public class UserDefinedColours extends Panel implements ActionListener,
AdjustmentListener, FocusListener
{
setTargetColour(colour);
okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
- frame.setTitle(MessageManager.getString("label.user_defined_colours") + " - " + label);
+ frame.setTitle(MessageManager.getString("label.user_defined_colours")
+ + " - " + label);
frame.setSize(420, 200);
}
// // not 1.1 compatible!
// dialog = new Dialog(((JVDialog)alignframe), title, true);
// } else {
- throw new Error(MessageManager.getString("label.error_unsupported_owwner_user_colour_scheme"));
+ throw new Error(
+ MessageManager
+ .getString("label.error_unsupported_owwner_user_colour_scheme"));
}
dialog.add(this);
import jalview.api.BuildDetailsI;
-
public class BuildDetails implements BuildDetailsI
{
private static String buildDate;
BuildDetails.installation = installation;
}
-
-
}
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties() {
+ public static Properties applicationProperties = new Properties()
+ {
// override results in properties output in alphabetical order
@Override
- public synchronized Enumeration<Object> keys() {
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ public synchronized Enumeration<Object> keys()
+ {
+ return Collections.enumeration(new TreeSet<Object>(super.keySet()));
}
};
fis = new FileInputStream(propertiesFile);
}
applicationProperties.load(fis);
-
+
// remove any old build properties
-
+
deleteBuildProperties();
fis.close();
} catch (Exception ex)
try
{
// Google analytics tracking code for Library Finder
- tracker = jgoogleanalyticstracker.getConstructor(new Class[]
- { String.class, String.class, String.class }).newInstance(
- new Object[]
- {
- "Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION")
- + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")), "UA-9060947-1" });
+ tracker = jgoogleanalyticstracker.getConstructor(
+ new Class[] { String.class, String.class, String.class })
+ .newInstance(
+ new Object[] {
+ "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION")
+ + "_"
+ + jalview.bin.Cache.getDefault(
+ "BUILD_DATE", "unknown")),
+ "UA-9060947-1" });
jgoogleanalyticstracker.getMethod("trackAsynchronously",
- new Class[]
- { trackerfocus }).invoke(tracker, new Object[]
- { trackerfocus.getConstructor(new Class[]
- { String.class }).newInstance(new Object[]
- { "Application Started." }) });
+ new Class[] { trackerfocus }).invoke(
+ tracker,
+ new Object[] { trackerfocus.getConstructor(
+ new Class[] { String.class }).newInstance(
+ new Object[] { "Application Started." }) });
} catch (RuntimeException e)
{
re = e;
}
else
{
- System.err
-.println("CMD [-noquestionnaire] executed successfully!");
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
}
desktop.checkForNews();
}
{
if (!headless)
{
- desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
System.out.println("CMD [-open " + file + "] executed successfully!");
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
{
- System.out
-.println("CMD [-sortbytree] executed successfully!");
+ System.out.println("CMD [-sortbytree] executed successfully!");
}
}
if (aparser.contains("no-annotation"))
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
- System.out
-.println("CMD no-annotation executed successfully!");
+ System.out.println("CMD no-annotation executed successfully!");
}
}
if (aparser.contains("nosortbytree"))
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, af });
+ executeGroovyScript(groovyscript, new Object[] { desktop, af });
System.out.println("CMD groovy[" + groovyscript
+ "] executed successfully!");
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, new Object[] { desktop,
+ startUpAlframe });
}
else
{
Object[] binding;
int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
+ String cnames[] = new String[] { "Jalview", "currentAlFrame" };
bspec = new Class[blen * 2];
binding = new Object[blen * 2];
blen = 0;
}
Class<?> gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor<?> gseccons = gsec.getConstructor(new Class[]
- { URL[].class }); // String[].class });
- Object gse = gseccons.newInstance(new Object[]
- { new URL[]
- { sfile } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.toString(), gbinding });
+ Constructor<?> gseccons = gsec
+ .getConstructor(new Class[] { URL[].class }); // String[].class
+ // });
+ Object gse = gseccons
+ .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
+ // } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.toString(), gbinding });
success = true;
} catch (Exception e)
{
running++;
}
- af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase()
- .equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
}
/**
* if true disable the check for jmol
}
else
{
- throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
AlignmentI al = null;
try
{
- al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
+ al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
+ format);
if ((al != null) && (al.getHeight() > 0))
{
dbgMsg("Successfully loaded file.");
if (protocol == AppletFormatAdapter.PASTE)
{
newAlignFrame.setTitle(MessageManager.formatMessage(
- "label.sequences_from", new Object[]
- { applet.getDocumentBase().toString() }));
+ "label.sequences_from", new Object[] { applet
+ .getDocumentBase().toString() }));
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[]
- { resolvedFile }));
+ "label.successfully_loaded_file",
+ new Object[] { resolvedFile }));
return newAlignFrame;
}
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
{
- seqs = new SequenceI[]
- { matcher == null ? (Sequence) alignFrame.getAlignViewport()
- .getAlignment().findName(sequence) : matcher
- .findIdMatch(sequence) };
+ seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment().findName(sequence)
+ : matcher.findIdMatch(sequence) };
}
}
}
else
{
- pdbs.addElement(new Object[]
- { pdb, seqs, chains, new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains,
+ new String(protocol) });
}
}
}
if (debug)
{
System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url
- + "'");
+ + "' to make: '" + url + "'");
}
return url;
}
if (url.indexOf("/") == 0)
{
String localfile = localref.getFile();
- url = codebase.substring(0, codebase.length()
- - localfile.length())
+ url = codebase.substring(0, codebase.length() - localfile.length())
+ url;
}
else
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Alignment implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _annotation.
- */
- private jalview.binding.Annotation _annotation;
-
- /**
- * Field _sequenceSet.
- */
- private jalview.binding.SequenceSet _sequenceSet;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public jalview.binding.Annotation getAnnotation(
- ) {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'sequenceSet'.
- *
- * @return the value of field 'SequenceSet'.
- */
- public jalview.binding.SequenceSet getSequenceSet(
- ) {
- return this._sequenceSet;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation the value of field 'annotation'.
- */
- public void setAnnotation(
- final jalview.binding.Annotation annotation) {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'sequenceSet'.
- *
- * @param sequenceSet the value of field 'sequenceSet'.
- */
- public void setSequenceSet(
- final jalview.binding.SequenceSet sequenceSet) {
- this._sequenceSet = sequenceSet;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Alignment
- */
- public static jalview.binding.Alignment unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class Alignment implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _annotation.
+ */
+ private jalview.binding.Annotation _annotation;
+
+ /**
+ * Field _sequenceSet.
+ */
+ private jalview.binding.SequenceSet _sequenceSet;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Alignment()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public jalview.binding.Annotation getAnnotation()
+ {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSet'.
+ *
+ * @return the value of field 'SequenceSet'.
+ */
+ public jalview.binding.SequenceSet getSequenceSet()
+ {
+ return this._sequenceSet;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation
+ * the value of field 'annotation'.
+ */
+ public void setAnnotation(final jalview.binding.Annotation annotation)
+ {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSet'.
+ *
+ * @param sequenceSet
+ * the value of field 'sequenceSet'.
+ */
+ public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
+ {
+ this._sequenceSet = sequenceSet;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Alignment
+ */
+ public static jalview.binding.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(
+ jalview.binding.Alignment.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Annotation implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _graph.
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _graphType.
- */
- private int _graphType;
-
- /**
- * keeps track of state for field: _graphType
- */
- private boolean _has_graphType;
-
- /**
- * Field _annotationElementList.
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Annotation() {
- super();
- this._annotationElementList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotationElement(
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationElementList.addElement(vAnnotationElement);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotationElement(
- final int index,
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationElementList.add(index, vAnnotationElement);
- }
-
- /**
- */
- public void deleteGraph(
- ) {
- this._has_graph= false;
- }
-
- /**
- */
- public void deleteGraphType(
- ) {
- this._has_graphType= false;
- }
-
- /**
- * Method enumerateAnnotationElement.
- *
- * @return an Enumeration over all
- * jalview.binding.AnnotationElement elements
- */
- public java.util.Enumeration enumerateAnnotationElement(
- ) {
- return this._annotationElementList.elements();
- }
-
- /**
- * Method getAnnotationElement.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.AnnotationElement
- * at the given index
- */
- public jalview.binding.AnnotationElement getAnnotationElement(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size()) {
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
- }
-
- return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
- }
-
- /**
- * Method getAnnotationElement.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.AnnotationElement[] getAnnotationElement(
- ) {
- jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
- return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
- }
-
- /**
- * Method getAnnotationElementCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationElementCount(
- ) {
- return this._annotationElementList.size();
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean getGraph(
- ) {
- return this._graph;
+public class Annotation implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Annotation()
+ {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph()
+ {
+ this._has_graph = false;
+ }
+
+ /**
+ */
+ public void deleteGraphType()
+ {
+ this._has_graphType = false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all jalview.binding.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.AnnotationElement at the given
+ * index
+ */
+ public jalview.binding.AnnotationElement getAnnotationElement(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
}
- /**
- * Returns the value of field 'graphType'.
- *
- * @return the value of field 'GraphType'.
- */
- public int getGraphType(
- ) {
- return this._graphType;
- }
-
- /**
- * Returns the value of field 'label'.
- *
- * @return the value of field 'Label'.
- */
- public java.lang.String getLabel(
- ) {
- return this._label;
- }
-
- /**
- * Method hasGraph.
- *
- * @return true if at least one Graph has been added
- */
- public boolean hasGraph(
- ) {
- return this._has_graph;
- }
-
- /**
- * Method hasGraphType.
- *
- * @return true if at least one GraphType has been added
- */
- public boolean hasGraphType(
- ) {
- return this._has_graphType;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean isGraph(
- ) {
- return this._graph;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllAnnotationElement(
- ) {
- this._annotationElementList.clear();
- }
-
- /**
- * Method removeAnnotationElement.
- *
- * @param vAnnotationElement
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotationElement(
- final jalview.binding.AnnotationElement vAnnotationElement) {
- boolean removed = _annotationElementList.remove(vAnnotationElement);
- return removed;
- }
-
- /**
- * Method removeAnnotationElementAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.AnnotationElement removeAnnotationElementAt(
- final int index) {
- java.lang.Object obj = this._annotationElementList.remove(index);
- return (jalview.binding.AnnotationElement) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAnnotationElement(
- final int index,
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size()) {
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
- }
-
- this._annotationElementList.set(index, vAnnotationElement);
- }
-
- /**
- *
- *
- * @param vAnnotationElementArray
- */
- public void setAnnotationElement(
- final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
- //-- copy array
- _annotationElementList.clear();
-
- for (int i = 0; i < vAnnotationElementArray.length; i++) {
- this._annotationElementList.add(vAnnotationElementArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
+ return (jalview.binding.AnnotationElement) _annotationElementList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.AnnotationElement[] getAnnotationElement()
+ {
+ jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+ return (jalview.binding.AnnotationElement[]) this._annotationElementList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount()
+ {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType()
+ {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType()
+ {
+ return this._has_graphType;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- * Sets the value of field 'graph'.
- *
- * @param graph the value of field 'graph'.
- */
- public void setGraph(
- final boolean graph) {
- this._graph = graph;
- this._has_graph = true;
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement()
+ {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.AnnotationElement removeAnnotationElementAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.binding.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
}
- /**
- * Sets the value of field 'graphType'.
- *
- * @param graphType the value of field 'graphType'.
- */
- public void setGraphType(
- final int graphType) {
- this._graphType = graphType;
- this._has_graphType = true;
- }
-
- /**
- * Sets the value of field 'label'.
- *
- * @param label the value of field 'label'.
- */
- public void setLabel(
- final java.lang.String label) {
- this._label = label;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Annotation
- */
- public static jalview.binding.Annotation unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.binding.AnnotationElement[] vAnnotationElementArray)
+ {
+ // -- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++)
+ {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph
+ * the value of field 'graph'.
+ */
+ public void setGraph(final boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType
+ * the value of field 'graphType'.
+ */
+ public void setGraphType(final int graphType)
+ {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label
+ * the value of field 'label'.
+ */
+ public void setLabel(final java.lang.String label)
+ {
+ this._label = label;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Annotation
+ */
+ public static jalview.binding.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(
+ jalview.binding.Annotation.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationElement implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _position.
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * Field _displayCharacter.
- */
- private java.lang.String _displayCharacter;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _secondaryStructure.
- */
- private java.lang.String _secondaryStructure;
-
- /**
- * Field _value.
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElement() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deletePosition(
- ) {
- this._has_position= false;
- }
-
- /**
- */
- public void deleteValue(
- ) {
- this._has_value= false;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'displayCharacter'.
- *
- * @return the value of field 'DisplayCharacter'.
- */
- public java.lang.String getDisplayCharacter(
- ) {
- return this._displayCharacter;
- }
-
- /**
- * Returns the value of field 'position'.
- *
- * @return the value of field 'Position'.
- */
- public int getPosition(
- ) {
- return this._position;
- }
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return the value of field 'SecondaryStructure'.
- */
- public java.lang.String getSecondaryStructure(
- ) {
- return this._secondaryStructure;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public float getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method hasPosition.
- *
- * @return true if at least one Position has been added
- */
- public boolean hasPosition(
- ) {
- return this._has_position;
- }
-
- /**
- * Method hasValue.
- *
- * @return true if at least one Value has been added
- */
- public boolean hasValue(
- ) {
- return this._has_value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
+public class AnnotationElement implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _position.
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _displayCharacter.
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure.
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationElement()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'displayCharacter'.
- *
- * @param displayCharacter the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(
- final java.lang.String displayCharacter) {
- this._displayCharacter = displayCharacter;
- }
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(
- final int position) {
- this._position = position;
- this._has_position = true;
- }
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure the value of field
- * 'secondaryStructure'.
- */
- public void setSecondaryStructure(
- final java.lang.String secondaryStructure) {
- this._secondaryStructure = secondaryStructure;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final float value) {
- this._value = value;
- this._has_value = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.AnnotationElement
- */
- public static jalview.binding.AnnotationElement unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
- }
+ public void deletePosition()
+ {
+ this._has_position = false;
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteValue()
+ {
+ this._has_value = false;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'displayCharacter'.
+ *
+ * @return the value of field 'DisplayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter()
+ {
+ return this._displayCharacter;
+ }
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return the value of field 'Position'.
+ */
+ public int getPosition()
+ {
+ return this._position;
+ }
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return the value of field 'SecondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure()
+ {
+ return this._secondaryStructure;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition()
+ {
+ return this._has_position;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue()
+ {
+ return this._has_value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'displayCharacter'.
+ *
+ * @param displayCharacter
+ * the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(final java.lang.String displayCharacter)
+ {
+ this._displayCharacter = displayCharacter;
+ }
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position
+ * the value of field 'position'.
+ */
+ public void setPosition(final int position)
+ {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure
+ * the value of field 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(
+ final java.lang.String secondaryStructure)
+ {
+ this._secondaryStructure = secondaryStructure;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final float value)
+ {
+ this._value = value;
+ this._has_value = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.AnnotationElement
+ */
+ public static jalview.binding.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
+ jalview.binding.AnnotationElement.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Colour implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _RGB.
- */
- private java.lang.String _RGB;
-
- /**
- * Field _minRGB.
- */
- private java.lang.String _minRGB;
-
- /**
- * loosely specified enumeration: NONE,ABOVE, or BELOW
- */
- private java.lang.String _threshType;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _max.
- */
- private float _max;
-
- /**
- * keeps track of state for field: _max
- */
- private boolean _has_max;
-
- /**
- * Field _min.
- */
- private float _min;
-
- /**
- * keeps track of state for field: _min
- */
- private boolean _has_min;
-
- /**
- * Field _colourByLabel.
- */
- private boolean _colourByLabel;
-
- /**
- * keeps track of state for field: _colourByLabel
- */
- private boolean _has_colourByLabel;
-
- /**
- * Field _autoScale.
- */
- private boolean _autoScale;
-
- /**
- * keeps track of state for field: _autoScale
- */
- private boolean _has_autoScale;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Colour() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAutoScale(
- ) {
- this._has_autoScale= false;
- }
-
- /**
- */
- public void deleteColourByLabel(
- ) {
- this._has_colourByLabel= false;
- }
-
- /**
- */
- public void deleteMax(
- ) {
- this._has_max= false;
- }
-
- /**
- */
- public void deleteMin(
- ) {
- this._has_min= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean getAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean getColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'max'.
- *
- * @return the value of field 'Max'.
- */
- public float getMax(
- ) {
- return this._max;
- }
-
- /**
- * Returns the value of field 'min'.
- *
- * @return the value of field 'Min'.
- */
- public float getMin(
- ) {
- return this._min;
- }
-
- /**
- * Returns the value of field 'minRGB'.
- *
- * @return the value of field 'MinRGB'.
- */
- public java.lang.String getMinRGB(
- ) {
- return this._minRGB;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'RGB'.
- *
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB(
- ) {
- return this._RGB;
- }
-
- /**
- * Returns the value of field 'threshType'. The field
- * 'threshType' has the following description: loosely
- * specified enumeration: NONE,ABOVE, or BELOW
- *
- * @return the value of field 'ThreshType'.
- */
- public java.lang.String getThreshType(
- ) {
- return this._threshType;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Method hasAutoScale.
- *
- * @return true if at least one AutoScale has been added
- */
- public boolean hasAutoScale(
- ) {
- return this._has_autoScale;
- }
-
- /**
- * Method hasColourByLabel.
- *
- * @return true if at least one ColourByLabel has been added
- */
- public boolean hasColourByLabel(
- ) {
- return this._has_colourByLabel;
- }
-
- /**
- * Method hasMax.
- *
- * @return true if at least one Max has been added
- */
- public boolean hasMax(
- ) {
- return this._has_max;
- }
-
- /**
- * Method hasMin.
- *
- * @return true if at least one Min has been added
- */
- public boolean hasMin(
- ) {
- return this._has_min;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean isAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean isColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'autoScale'.
- *
- * @param autoScale the value of field 'autoScale'.
- */
- public void setAutoScale(
- final boolean autoScale) {
- this._autoScale = autoScale;
- this._has_autoScale = true;
- }
-
- /**
- * Sets the value of field 'colourByLabel'.
- *
- * @param colourByLabel the value of field 'colourByLabel'.
- */
- public void setColourByLabel(
- final boolean colourByLabel) {
- this._colourByLabel = colourByLabel;
- this._has_colourByLabel = true;
- }
-
- /**
- * Sets the value of field 'max'.
- *
- * @param max the value of field 'max'.
- */
- public void setMax(
- final float max) {
- this._max = max;
- this._has_max = true;
- }
-
- /**
- * Sets the value of field 'min'.
- *
- * @param min the value of field 'min'.
- */
- public void setMin(
- final float min) {
- this._min = min;
- this._has_min = true;
- }
-
- /**
- * Sets the value of field 'minRGB'.
- *
- * @param minRGB the value of field 'minRGB'.
- */
- public void setMinRGB(
- final java.lang.String minRGB) {
- this._minRGB = minRGB;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB the value of field 'RGB'.
- */
- public void setRGB(
- final java.lang.String RGB) {
- this._RGB = RGB;
- }
-
- /**
- * Sets the value of field 'threshType'. The field 'threshType'
- * has the following description: loosely specified
- * enumeration: NONE,ABOVE, or BELOW
- *
- * @param threshType the value of field 'threshType'.
- */
- public void setThreshType(
- final java.lang.String threshType) {
- this._threshType = threshType;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Colour
- */
- public static jalview.binding.Colour unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Colour implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+
+ /**
+ * loosely specified enumeration: NONE,ABOVE, or BELOW
+ */
+ private java.lang.String _threshType;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Colour()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAutoScale()
+ {
+ this._has_autoScale = false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel()
+ {
+ this._has_colourByLabel = false;
+ }
+
+ /**
+ */
+ public void deleteMax()
+ {
+ this._has_max = false;
+ }
+
+ /**
+ */
+ public void deleteMin()
+ {
+ this._has_min = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax()
+ {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin()
+ {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB()
+ {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB()
+ {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'. The field 'threshType' has the
+ * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public java.lang.String getThreshType()
+ {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale()
+ {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel()
+ {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax()
+ {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin()
+ {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale
+ * the value of field 'autoScale'.
+ */
+ public void setAutoScale(final boolean autoScale)
+ {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel
+ * the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(final boolean colourByLabel)
+ {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max
+ * the value of field 'max'.
+ */
+ public void setMax(final float max)
+ {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min
+ * the value of field 'min'.
+ */
+ public void setMin(final float min)
+ {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB
+ * the value of field 'minRGB'.
+ */
+ public void setMinRGB(final java.lang.String minRGB)
+ {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB
+ * the value of field 'RGB'.
+ */
+ public void setRGB(final java.lang.String RGB)
+ {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'. The field 'threshType' has the
+ * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @param threshType
+ * the value of field 'threshType'.
+ */
+ public void setThreshType(final java.lang.String threshType)
+ {
+ this._threshType = threshType;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(
+ jalview.binding.Colour.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Feature implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _begin.
- */
- private int _begin;
-
- /**
- * keeps track of state for field: _begin
- */
- private boolean _has_begin;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _status.
- */
- private java.lang.String _status;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Feature() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteBegin(
- ) {
- this._has_begin= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return the value of field 'Begin'.
- */
- public int getBegin(
- ) {
- return this._begin;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'status'.
- *
- * @return the value of field 'Status'.
- */
- public java.lang.String getStatus(
- ) {
- return this._status;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method hasBegin.
- *
- * @return true if at least one Begin has been added
- */
- public boolean hasBegin(
- ) {
- return this._has_begin;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
+public class Feature implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Feature()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin the value of field 'begin'.
- */
- public void setBegin(
- final int begin) {
- this._begin = begin;
- this._has_begin = true;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'status'.
- *
- * @param status the value of field 'status'.
- */
- public void setStatus(
- final java.lang.String status) {
- this._status = status;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
- }
+ public void deleteBegin()
+ {
+ this._has_begin = false;
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin()
+ {
+ return this._begin;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus()
+ {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin()
+ {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin
+ * the value of field 'begin'.
+ */
+ public void setBegin(final int begin)
+ {
+ this._begin = begin;
+ this._has_begin = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status
+ * the value of field 'status'.
+ */
+ public void setStatus(final java.lang.String status)
+ {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(
+ jalview.binding.Feature.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class FeatureSettings implements java.io.Serializable {
+public class FeatureSettings implements java.io.Serializable
+{
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
- /**
- * Field _settingList.
- */
- private java.util.Vector _settingList;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public FeatureSettings()
+ {
+ super();
+ this._settingList = new java.util.Vector();
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public FeatureSettings() {
- super();
- this._settingList = new java.util.Vector();
- }
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.addElement(vSetting);
+ }
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.add(index, vSetting);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.binding.Setting elements
+ */
+ public java.util.Enumeration enumerateSetting()
+ {
+ return this._settingList.elements();
+ }
- /**
- *
- *
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSetting(
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- this._settingList.addElement(vSetting);
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Setting at the given index
+ */
+ public jalview.binding.Setting getSetting(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("getSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSetting(
- final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- this._settingList.add(index, vSetting);
- }
+ return (jalview.binding.Setting) _settingList.get(index);
+ }
- /**
- * Method enumerateSetting.
- *
- * @return an Enumeration over all jalview.binding.Setting
- * elements
- */
- public java.util.Enumeration enumerateSetting(
- ) {
- return this._settingList.elements();
- }
+ /**
+ * Method getSetting.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Setting[] getSetting()
+ {
+ jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+ return (jalview.binding.Setting[]) this._settingList.toArray(array);
+ }
- /**
- * Method getSetting.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Setting at the
- * given index
- */
- public jalview.binding.Setting getSetting(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size()) {
- throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
- }
-
- return (jalview.binding.Setting) _settingList.get(index);
- }
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount()
+ {
+ return this._settingList.size();
+ }
- /**
- * Method getSetting.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Setting[] getSetting(
- ) {
- jalview.binding.Setting[] array = new jalview.binding.Setting[0];
- return (jalview.binding.Setting[]) this._settingList.toArray(array);
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- * Method getSettingCount.
- *
- * @return the size of this collection
- */
- public int getSettingCount(
- ) {
- return this._settingList.size();
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ public void removeAllSetting()
+ {
+ this._settingList.clear();
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(final jalview.binding.Setting vSetting)
+ {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
+ }
- /**
- */
- public void removeAllSetting(
- ) {
- this._settingList.clear();
- }
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Setting removeSettingAt(final int index)
+ {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.binding.Setting) obj;
+ }
- /**
- * Method removeSetting.
- *
- * @param vSetting
- * @return true if the object was removed from the collection.
- */
- public boolean removeSetting(
- final jalview.binding.Setting vSetting) {
- boolean removed = _settingList.remove(vSetting);
- return removed;
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSetting(final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("setSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
- /**
- * Method removeSettingAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Setting removeSettingAt(
- final int index) {
- java.lang.Object obj = this._settingList.remove(index);
- return (jalview.binding.Setting) obj;
- }
+ this._settingList.set(index, vSetting);
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSetting(
- final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size()) {
- throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
- }
-
- this._settingList.set(index, vSetting);
- }
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(final jalview.binding.Setting[] vSettingArray)
+ {
+ // -- copy array
+ _settingList.clear();
- /**
- *
- *
- * @param vSettingArray
- */
- public void setSetting(
- final jalview.binding.Setting[] vSettingArray) {
- //-- copy array
- _settingList.clear();
-
- for (int i = 0; i < vSettingArray.length; i++) {
- this._settingList.add(vSettingArray[i]);
- }
+ for (int i = 0; i < vSettingArray.length; i++)
+ {
+ this._settingList.add(vSettingArray[i]);
}
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.FeatureSettings
- */
- public static jalview.binding.FeatureSettings unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.FeatureSettings
+ */
+ public static jalview.binding.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
+ jalview.binding.FeatureSettings.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Features extends Feature
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Features() {
- super();
- }
-
+ public Features()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(
+ jalview.binding.Features.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JGroup implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _colour.
- */
- private java.lang.String _colour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _outlineColour.
- */
- private int _outlineColour;
-
- /**
- * keeps track of state for field: _outlineColour
- */
- private boolean _has_outlineColour;
-
- /**
- * Field _displayBoxes.
- */
- private boolean _displayBoxes;
-
- /**
- * keeps track of state for field: _displayBoxes
- */
- private boolean _has_displayBoxes;
-
- /**
- * Field _displayText.
- */
- private boolean _displayText;
-
- /**
- * keeps track of state for field: _displayText
- */
- private boolean _has_displayText;
-
- /**
- * Field _colourText.
- */
- private boolean _colourText;
-
- /**
- * keeps track of state for field: _colourText
- */
- private boolean _has_colourText;
-
- /**
- * Field _seqList.
- */
- private java.util.Vector _seqList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JGroup() {
- super();
- this._seqList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.addElement(new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final int index,
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.add(index, new java.lang.Integer(vSeq));
- }
-
- /**
- */
- public void deleteColourText(
- ) {
- this._has_colourText= false;
- }
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteDisplayBoxes(
- ) {
- this._has_displayBoxes= false;
- }
-
- /**
- */
- public void deleteDisplayText(
- ) {
- this._has_displayText= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteOutlineColour(
- ) {
- this._has_outlineColour= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Method enumerateSeq.
- *
- * @return an Enumeration over all int elements
- */
- public java.util.Enumeration enumerateSeq(
- ) {
- return this._seqList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public java.lang.String getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean getColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean getDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean getDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return the value of field 'OutlineColour'.
- */
- public int getOutlineColour(
- ) {
- return this._outlineColour;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Method getSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the int at the given index
- */
- public int getSeq(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- return ((java.lang.Integer) _seqList.get(index)).intValue();
- }
-
- /**
- * Method getSeq.Returns the contents of the collection in an
- * Array.
- *
- * @return this collection as an Array
- */
- public int[] getSeq(
- ) {
- int size = this._seqList.size();
- int[] array = new int[size];
- java.util.Iterator iter = _seqList.iterator();
- for (int index = 0; index < size; index++) {
- array[index] = ((java.lang.Integer) iter.next()).intValue();
- }
- return array;
- }
-
- /**
- * Method getSeqCount.
- *
- * @return the size of this collection
- */
- public int getSeqCount(
- ) {
- return this._seqList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasColourText.
- *
- * @return true if at least one ColourText has been added
- */
- public boolean hasColourText(
- ) {
- return this._has_colourText;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasDisplayBoxes.
- *
- * @return true if at least one DisplayBoxes has been added
- */
- public boolean hasDisplayBoxes(
- ) {
- return this._has_displayBoxes;
- }
-
- /**
- * Method hasDisplayText.
- *
- * @return true if at least one DisplayText has been added
- */
- public boolean hasDisplayText(
- ) {
- return this._has_displayText;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasOutlineColour.
- *
- * @return true if at least one OutlineColour has been added
- */
- public boolean hasOutlineColour(
- ) {
- return this._has_outlineColour;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean isColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean isDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean isDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllSeq(
- ) {
- this._seqList.clear();
- }
-
- /**
- * Method removeSeq.
- *
- * @param vSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeSeq(
- final int vSeq) {
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
- return removed;
- }
-
- /**
- * Method removeSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public int removeSeqAt(
- final int index) {
- java.lang.Object obj = this._seqList.remove(index);
- return ((java.lang.Integer) obj).intValue();
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final java.lang.String colour) {
- this._colour = colour;
- }
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText the value of field 'colourText'.
- */
- public void setColourText(
- final boolean colourText) {
- this._colourText = colourText;
- this._has_colourText = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(
- final boolean displayBoxes) {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- }
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText the value of field 'displayText'.
- */
- public void setDisplayText(
- final boolean displayText) {
- this._displayText = displayText;
- this._has_displayText = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour the value of field 'outlineColour'.
- */
- public void setOutlineColour(
- final int outlineColour) {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSeq(
- final int index,
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- this._seqList.set(index, new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param vSeqArray
- */
- public void setSeq(
- final int[] vSeqArray) {
- //-- copy array
- _seqList.clear();
-
- for (int i = 0; i < vSeqArray.length; i++) {
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JGroup
- */
- public static jalview.binding.JGroup unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JGroup implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroup()
+ {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText()
+ {
+ this._has_colourText = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes()
+ {
+ this._has_displayBoxes = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText()
+ {
+ this._has_displayText = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour()
+ {
+ this._has_outlineColour = false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq()
+ {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour()
+ {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq()
+ {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount()
+ {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText()
+ {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes()
+ {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText()
+ {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour()
+ {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSeq()
+ {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(final int vSeq)
+ {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(final int index)
+ {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final java.lang.String colour)
+ {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText
+ * the value of field 'colourText'.
+ */
+ public void setColourText(final boolean colourText)
+ {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes
+ * the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(final boolean displayBoxes)
+ {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText
+ * the value of field 'displayText'.
+ */
+ public void setDisplayText(final boolean displayText)
+ {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour
+ * the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(final int outlineColour)
+ {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(final int[] vSeqArray)
+ {
+ // -- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++)
+ {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(
+ jalview.binding.JGroup.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JSeq implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _id.
- */
- private int _id;
-
- /**
- * keeps track of state for field: _id
- */
- private boolean _has_id;
-
- /**
- * Field _featuresList.
- */
- private java.util.Vector _featuresList;
-
- /**
- * Field _pdbidsList.
- */
- private java.util.Vector _pdbidsList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JSeq() {
- super();
- this._featuresList = new java.util.Vector();
- this._pdbidsList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addFeatures(
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- this._featuresList.addElement(vFeatures);
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addFeatures(
- final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- this._featuresList.add(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbids(
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- this._pdbidsList.addElement(vPdbids);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbids(
- final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- this._pdbidsList.add(index, vPdbids);
- }
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteId(
- ) {
- this._has_id= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Method enumerateFeatures.
- *
- * @return an Enumeration over all jalview.binding.Features
- * elements
- */
- public java.util.Enumeration enumerateFeatures(
- ) {
- return this._featuresList.elements();
- }
-
- /**
- * Method enumeratePdbids.
- *
- * @return an Enumeration over all jalview.binding.Pdbids
- * elements
- */
- public java.util.Enumeration enumeratePdbids(
- ) {
- return this._pdbidsList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Method getFeatures.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Features at the
- * given index
- */
- public jalview.binding.Features getFeatures(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size()) {
- throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
- }
-
- return (jalview.binding.Features) _featuresList.get(index);
- }
-
- /**
- * Method getFeatures.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Features[] getFeatures(
- ) {
- jalview.binding.Features[] array = new jalview.binding.Features[0];
- return (jalview.binding.Features[]) this._featuresList.toArray(array);
- }
-
- /**
- * Method getFeaturesCount.
- *
- * @return the size of this collection
- */
- public int getFeaturesCount(
- ) {
- return this._featuresList.size();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public int getId(
- ) {
- return this._id;
- }
-
- /**
- * Method getPdbids.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Pdbids at the given
- * index
- */
- public jalview.binding.Pdbids getPdbids(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size()) {
- throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
- }
-
- return (jalview.binding.Pdbids) _pdbidsList.get(index);
- }
-
- /**
- * Method getPdbids.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Pdbids[] getPdbids(
- ) {
- jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
- return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
- }
-
- /**
- * Method getPdbidsCount.
- *
- * @return the size of this collection
- */
- public int getPdbidsCount(
- ) {
- return this._pdbidsList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasId.
- *
- * @return true if at least one Id has been added
- */
- public boolean hasId(
- ) {
- return this._has_id;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllFeatures(
- ) {
- this._featuresList.clear();
- }
-
- /**
- */
- public void removeAllPdbids(
- ) {
- this._pdbidsList.clear();
- }
-
- /**
- * Method removeFeatures.
- *
- * @param vFeatures
- * @return true if the object was removed from the collection.
- */
- public boolean removeFeatures(
- final jalview.binding.Features vFeatures) {
- boolean removed = _featuresList.remove(vFeatures);
- return removed;
- }
-
- /**
- * Method removeFeaturesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Features removeFeaturesAt(
- final int index) {
- java.lang.Object obj = this._featuresList.remove(index);
- return (jalview.binding.Features) obj;
- }
-
- /**
- * Method removePdbids.
- *
- * @param vPdbids
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbids(
- final jalview.binding.Pdbids vPdbids) {
- boolean removed = _pdbidsList.remove(vPdbids);
- return removed;
- }
-
- /**
- * Method removePdbidsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Pdbids removePdbidsAt(
- final int index) {
- java.lang.Object obj = this._pdbidsList.remove(index);
- return (jalview.binding.Pdbids) obj;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setFeatures(
- final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size()) {
- throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
- }
-
- this._featuresList.set(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vFeaturesArray
- */
- public void setFeatures(
- final jalview.binding.Features[] vFeaturesArray) {
- //-- copy array
- _featuresList.clear();
-
- for (int i = 0; i < vFeaturesArray.length; i++) {
- this._featuresList.add(vFeaturesArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final int id) {
- this._id = id;
- this._has_id = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setPdbids(
- final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size()) {
- throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
- }
-
- this._pdbidsList.set(index, vPdbids);
- }
-
- /**
- *
- *
- * @param vPdbidsArray
- */
- public void setPdbids(
- final jalview.binding.Pdbids[] vPdbidsArray) {
- //-- copy array
- _pdbidsList.clear();
-
- for (int i = 0; i < vPdbidsArray.length; i++) {
- this._pdbidsList.add(vPdbidsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JSeq
- */
- public static jalview.binding.JSeq unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JSeq implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _id.
+ */
+ private int _id;
+
+ /**
+ * keeps track of state for field: _id
+ */
+ private boolean _has_id;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JSeq()
+ {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteId()
+ {
+ this._has_id = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.binding.Features elements
+ */
+ public java.util.Enumeration enumerateFeatures()
+ {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.binding.Pdbids elements
+ */
+ public java.util.Enumeration enumeratePdbids()
+ {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Features at the given index
+ */
+ public jalview.binding.Features getFeatures(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size())
+ {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Features[] getFeatures()
+ {
+ jalview.binding.Features[] array = new jalview.binding.Features[0];
+ return (jalview.binding.Features[]) this._featuresList.toArray(array);
+ }
+
+ /**
+ * Method getFeaturesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFeaturesCount()
+ {
+ return this._featuresList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public int getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbids.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Pdbids at the given index
+ */
+ public jalview.binding.Pdbids getPdbids(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size())
+ {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Pdbids[] getPdbids()
+ {
+ jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+ return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+ }
+
+ /**
+ * Method getPdbidsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbidsCount()
+ {
+ return this._pdbidsList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasId.
+ *
+ * @return true if at least one Id has been added
+ */
+ public boolean hasId()
+ {
+ return this._has_id;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllFeatures()
+ {
+ this._featuresList.clear();
+ }
+
+ /**
+ */
+ public void removeAllPdbids()
+ {
+ this._pdbidsList.clear();
+ }
+
+ /**
+ * Method removeFeatures.
+ *
+ * @param vFeatures
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFeatures(final jalview.binding.Features vFeatures)
+ {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Features removeFeaturesAt(final int index)
+ {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.binding.Features) obj;
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(final jalview.binding.Pdbids vPdbids)
+ {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Pdbids removePdbidsAt(final int index)
+ {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.binding.Pdbids) obj;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setFeatures(final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size())
+ {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(final jalview.binding.Features[] vFeaturesArray)
+ {
+ // -- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++)
+ {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final int id)
+ {
+ this._id = id;
+ this._has_id = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPdbids(final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size())
+ {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray)
+ {
+ // -- copy array
+ _pdbidsList.clear();
+
+ for (int i = 0; i < vPdbidsArray.length; i++)
+ {
+ this._pdbidsList.add(vPdbidsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JSeq
+ */
+ public static jalview.binding.JSeq unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(
+ jalview.binding.JSeq.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModel implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _creationDate.
- */
- private java.util.Date _creationDate;
-
- /**
- * Field _version.
- */
- private java.lang.String _version;
-
- /**
- * Field _vamsasModel.
- */
- private jalview.binding.VamsasModel _vamsasModel;
-
- /**
- * Field _jalviewModelSequence.
- */
- private jalview.binding.JalviewModelSequence _jalviewModelSequence;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModel() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'creationDate'.
- *
- * @return the value of field 'CreationDate'.
- */
- public java.util.Date getCreationDate(
- ) {
- return this._creationDate;
- }
-
- /**
- * Returns the value of field 'jalviewModelSequence'.
- *
- * @return the value of field 'JalviewModelSequence'.
- */
- public jalview.binding.JalviewModelSequence getJalviewModelSequence(
- ) {
- return this._jalviewModelSequence;
- }
-
- /**
- * Returns the value of field 'vamsasModel'.
- *
- * @return the value of field 'VamsasModel'.
- */
- public jalview.binding.VamsasModel getVamsasModel(
- ) {
- return this._vamsasModel;
- }
-
- /**
- * Returns the value of field 'version'.
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'creationDate'.
- *
- * @param creationDate the value of field 'creationDate'.
- */
- public void setCreationDate(
- final java.util.Date creationDate) {
- this._creationDate = creationDate;
- }
-
- /**
- * Sets the value of field 'jalviewModelSequence'.
- *
- * @param jalviewModelSequence the value of field
- * 'jalviewModelSequence'.
- */
- public void setJalviewModelSequence(
- final jalview.binding.JalviewModelSequence jalviewModelSequence) {
- this._jalviewModelSequence = jalviewModelSequence;
- }
-
- /**
- * Sets the value of field 'vamsasModel'.
- *
- * @param vamsasModel the value of field 'vamsasModel'.
- */
- public void setVamsasModel(
- final jalview.binding.VamsasModel vamsasModel) {
- this._vamsasModel = vamsasModel;
- }
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewModel
- */
- public static jalview.binding.JalviewModel unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _creationDate.
+ */
+ private java.util.Date _creationDate;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _vamsasModel.
+ */
+ private jalview.binding.VamsasModel _vamsasModel;
+
+ /**
+ * Field _jalviewModelSequence.
+ */
+ private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModel()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'creationDate'.
+ *
+ * @return the value of field 'CreationDate'.
+ */
+ public java.util.Date getCreationDate()
+ {
+ return this._creationDate;
+ }
+
+ /**
+ * Returns the value of field 'jalviewModelSequence'.
+ *
+ * @return the value of field 'JalviewModelSequence'.
+ */
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence()
+ {
+ return this._jalviewModelSequence;
+ }
+
+ /**
+ * Returns the value of field 'vamsasModel'.
+ *
+ * @return the value of field 'VamsasModel'.
+ */
+ public jalview.binding.VamsasModel getVamsasModel()
+ {
+ return this._vamsasModel;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'creationDate'.
+ *
+ * @param creationDate
+ * the value of field 'creationDate'.
+ */
+ public void setCreationDate(final java.util.Date creationDate)
+ {
+ this._creationDate = creationDate;
+ }
+
+ /**
+ * Sets the value of field 'jalviewModelSequence'.
+ *
+ * @param jalviewModelSequence
+ * the value of field 'jalviewModelSequence'.
+ */
+ public void setJalviewModelSequence(
+ final jalview.binding.JalviewModelSequence jalviewModelSequence)
+ {
+ this._jalviewModelSequence = jalviewModelSequence;
+ }
+
+ /**
+ * Sets the value of field 'vamsasModel'.
+ *
+ * @param vamsasModel
+ * the value of field 'vamsasModel'.
+ */
+ public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel)
+ {
+ this._vamsasModel = vamsasModel;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModel
+ */
+ public static jalview.binding.JalviewModel unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
+ jalview.binding.JalviewModel.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequence implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _JSeqList.
- */
- private java.util.Vector _JSeqList;
-
- /**
- * Field _JGroupList.
- */
- private java.util.Vector _JGroupList;
-
- /**
- * Field _viewportList.
- */
- private java.util.Vector _viewportList;
-
- /**
- * Field _userColoursList.
- */
- private java.util.Vector _userColoursList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _featureSettings.
- */
- private jalview.binding.FeatureSettings _featureSettings;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModelSequence() {
- super();
- this._JSeqList = new java.util.Vector();
- this._JGroupList = new java.util.Vector();
- this._viewportList = new java.util.Vector();
- this._userColoursList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJGroup(
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._JGroupList.addElement(vJGroup);
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJGroup(
- final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._JGroupList.add(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJSeq(
- final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._JSeqList.addElement(vJSeq);
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJSeq(
- final int index,
- final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._JSeqList.add(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- *
- *
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addUserColours(
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- this._userColoursList.addElement(vUserColours);
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addUserColours(
- final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- this._userColoursList.add(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addViewport(
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- this._viewportList.addElement(vViewport);
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addViewport(
- final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- this._viewportList.add(index, vViewport);
- }
-
- /**
- * Method enumerateJGroup.
- *
- * @return an Enumeration over all jalview.binding.JGroup
- * elements
- */
- public java.util.Enumeration enumerateJGroup(
- ) {
- return this._JGroupList.elements();
- }
-
- /**
- * Method enumerateJSeq.
- *
- * @return an Enumeration over all jalview.binding.JSeq elements
- */
- public java.util.Enumeration enumerateJSeq(
- ) {
- return this._JSeqList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all jalview.binding.Tree elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
- }
-
- /**
- * Method enumerateUserColours.
- *
- * @return an Enumeration over all jalview.binding.UserColours
- * elements
- */
- public java.util.Enumeration enumerateUserColours(
- ) {
- return this._userColoursList.elements();
- }
-
- /**
- * Method enumerateViewport.
- *
- * @return an Enumeration over all jalview.binding.Viewport
- * elements
- */
- public java.util.Enumeration enumerateViewport(
- ) {
- return this._viewportList.elements();
- }
-
- /**
- * Returns the value of field 'featureSettings'.
- *
- * @return the value of field 'FeatureSettings'.
- */
- public jalview.binding.FeatureSettings getFeatureSettings(
- ) {
- return this._featureSettings;
- }
-
- /**
- * Method getJGroup.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.JGroup at the given
- * index
- */
- public jalview.binding.JGroup getJGroup(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size()) {
- throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
- }
-
- return (jalview.binding.JGroup) _JGroupList.get(index);
- }
-
- /**
- * Method getJGroup.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.JGroup[] getJGroup(
- ) {
- jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
- return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
- }
-
- /**
- * Method getJGroupCount.
- *
- * @return the size of this collection
- */
- public int getJGroupCount(
- ) {
- return this._JGroupList.size();
- }
-
- /**
- * Method getJSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.JSeq at the given
- * index
- */
- public jalview.binding.JSeq getJSeq(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size()) {
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- return (jalview.binding.JSeq) _JSeqList.get(index);
- }
-
- /**
- * Method getJSeq.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.JSeq[] getJSeq(
- ) {
- jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
- return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
- }
-
- /**
- * Method getJSeqCount.
- *
- * @return the size of this collection
- */
- public int getJSeqCount(
- ) {
- return this._JSeqList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Tree at the given
- * index
- */
- public jalview.binding.Tree getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (jalview.binding.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Tree[] getTree(
- ) {
- jalview.binding.Tree[] array = new jalview.binding.Tree[0];
- return (jalview.binding.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Method getUserColours.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.UserColours at the
- * given index
- */
- public jalview.binding.UserColours getUserColours(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size()) {
- throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
- }
-
- return (jalview.binding.UserColours) _userColoursList.get(index);
- }
-
- /**
- * Method getUserColours.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.UserColours[] getUserColours(
- ) {
- jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
- return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
- }
-
- /**
- * Method getUserColoursCount.
- *
- * @return the size of this collection
- */
- public int getUserColoursCount(
- ) {
- return this._userColoursList.size();
- }
-
- /**
- * Method getViewport.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Viewport at the
- * given index
- */
- public jalview.binding.Viewport getViewport(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size()) {
- throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
- }
-
- return (jalview.binding.Viewport) _viewportList.get(index);
- }
-
- /**
- * Method getViewport.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Viewport[] getViewport(
- ) {
- jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
- return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
- }
-
- /**
- * Method getViewportCount.
- *
- * @return the size of this collection
- */
- public int getViewportCount(
- ) {
- return this._viewportList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllJGroup(
- ) {
- this._JGroupList.clear();
- }
-
- /**
- */
- public void removeAllJSeq(
- ) {
- this._JSeqList.clear();
- }
-
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- */
- public void removeAllUserColours(
- ) {
- this._userColoursList.clear();
- }
-
- /**
- */
- public void removeAllViewport(
- ) {
- this._viewportList.clear();
- }
-
- /**
- * Method removeJGroup.
- *
- * @param vJGroup
- * @return true if the object was removed from the collection.
- */
- public boolean removeJGroup(
- final jalview.binding.JGroup vJGroup) {
- boolean removed = _JGroupList.remove(vJGroup);
- return removed;
- }
-
- /**
- * Method removeJGroupAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JGroup removeJGroupAt(
- final int index) {
- java.lang.Object obj = this._JGroupList.remove(index);
- return (jalview.binding.JGroup) obj;
- }
-
- /**
- * Method removeJSeq.
- *
- * @param vJSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeJSeq(
- final jalview.binding.JSeq vJSeq) {
- boolean removed = _JSeqList.remove(vJSeq);
- return removed;
- }
-
- /**
- * Method removeJSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JSeq removeJSeqAt(
- final int index) {
- java.lang.Object obj = this._JSeqList.remove(index);
- return (jalview.binding.JSeq) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final jalview.binding.Tree vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Tree removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (jalview.binding.Tree) obj;
- }
-
- /**
- * Method removeUserColours.
- *
- * @param vUserColours
- * @return true if the object was removed from the collection.
- */
- public boolean removeUserColours(
- final jalview.binding.UserColours vUserColours) {
- boolean removed = _userColoursList.remove(vUserColours);
- return removed;
- }
-
- /**
- * Method removeUserColoursAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.UserColours removeUserColoursAt(
- final int index) {
- java.lang.Object obj = this._userColoursList.remove(index);
- return (jalview.binding.UserColours) obj;
- }
-
- /**
- * Method removeViewport.
- *
- * @param vViewport
- * @return true if the object was removed from the collection.
- */
- public boolean removeViewport(
- final jalview.binding.Viewport vViewport) {
- boolean removed = _viewportList.remove(vViewport);
- return removed;
- }
-
- /**
- * Method removeViewportAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Viewport removeViewportAt(
- final int index) {
- java.lang.Object obj = this._viewportList.remove(index);
- return (jalview.binding.Viewport) obj;
- }
-
- /**
- * Sets the value of field 'featureSettings'.
- *
- * @param featureSettings the value of field 'featureSettings'.
- */
- public void setFeatureSettings(
- final jalview.binding.FeatureSettings featureSettings) {
- this._featureSettings = featureSettings;
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setJGroup(
- final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size()) {
- throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
- }
-
- this._JGroupList.set(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJGroupArray
- */
- public void setJGroup(
- final jalview.binding.JGroup[] vJGroupArray) {
- //-- copy array
- _JGroupList.clear();
-
- for (int i = 0; i < vJGroupArray.length; i++) {
- this._JGroupList.add(vJGroupArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setJSeq(
- final int index,
- final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size()) {
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- this._JSeqList.set(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vJSeqArray
- */
- public void setJSeq(
- final jalview.binding.JSeq[] vJSeqArray) {
- //-- copy array
- _JSeqList.clear();
-
- for (int i = 0; i < vJSeqArray.length; i++) {
- this._JSeqList.add(vJSeqArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTree(
- final int index,
- final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final jalview.binding.Tree[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setUserColours(
- final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size()) {
- throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
- }
-
- this._userColoursList.set(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vUserColoursArray
- */
- public void setUserColours(
- final jalview.binding.UserColours[] vUserColoursArray) {
- //-- copy array
- _userColoursList.clear();
-
- for (int i = 0; i < vUserColoursArray.length; i++) {
- this._userColoursList.add(vUserColoursArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setViewport(
- final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size()) {
- throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
- }
-
- this._viewportList.set(index, vViewport);
- }
-
- /**
- *
- *
- * @param vViewportArray
- */
- public void setViewport(
- final jalview.binding.Viewport[] vViewportArray) {
- //-- copy array
- _viewportList.clear();
-
- for (int i = 0; i < vViewportArray.length; i++) {
- this._viewportList.add(vViewportArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewModelSequence
- */
- public static jalview.binding.JalviewModelSequence unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.binding.FeatureSettings _featureSettings;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModelSequence()
+ {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index, final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.binding.JGroup elements
+ */
+ public java.util.Enumeration enumerateJGroup()
+ {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.binding.JSeq elements
+ */
+ public java.util.Enumeration enumerateJSeq()
+ {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.binding.Tree elements
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.binding.UserColours elements
+ */
+ public java.util.Enumeration enumerateUserColours()
+ {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.binding.Viewport elements
+ */
+ public java.util.Enumeration enumerateViewport()
+ {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.binding.FeatureSettings getFeatureSettings()
+ {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JGroup at the given index
+ */
+ public jalview.binding.JGroup getJGroup(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JGroup[] getJGroup()
+ {
+ jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+ return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount()
+ {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JSeq at the given index
+ */
+ public jalview.binding.JSeq getJSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JSeq[] getJSeq()
+ {
+ jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+ return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount()
+ {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Tree at the given index
+ */
+ public jalview.binding.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Tree[] getTree()
+ {
+ jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+ return (jalview.binding.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount()
+ {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.UserColours at the given index
+ */
+ public jalview.binding.UserColours getUserColours(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.UserColours) _userColoursList.get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.UserColours[] getUserColours()
+ {
+ jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+ return (jalview.binding.UserColours[]) this._userColoursList
+ .toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount()
+ {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Viewport at the given index
+ */
+ public jalview.binding.Viewport getViewport(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("getViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Viewport) _viewportList.get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Viewport[] getViewport()
+ {
+ jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+ return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount()
+ {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup()
+ {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq()
+ {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours()
+ {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport()
+ {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
+ {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JGroup removeJGroupAt(final int index)
+ {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.binding.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
+ {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JSeq removeJSeqAt(final int index)
+ {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.binding.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final jalview.binding.Tree vTree)
+ {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Tree removeTreeAt(final int index)
+ {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.binding.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.binding.UserColours vUserColours)
+ {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.UserColours removeUserColoursAt(final int index)
+ {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.binding.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(final jalview.binding.Viewport vViewport)
+ {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Viewport removeViewportAt(final int index)
+ {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.binding.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings
+ * the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.binding.FeatureSettings featureSettings)
+ {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJGroup(final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
+ {
+ // -- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++)
+ {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
+ {
+ // -- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++)
+ {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index, final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final jalview.binding.Tree[] vTreeArray)
+ {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++)
+ {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setUserColours(final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.binding.UserColours[] vUserColoursArray)
+ {
+ // -- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++)
+ {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setViewport(final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("setViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(final jalview.binding.Viewport[] vViewportArray)
+ {
+ // -- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++)
+ {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModelSequence
+ */
+ public static jalview.binding.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
+ jalview.binding.JalviewModelSequence.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewUserColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _schemeName.
- */
- private java.lang.String _schemeName;
-
- /**
- * Jalview colour scheme document version.
- *
- */
- private java.lang.String _version;
-
- /**
- * Field _colourList.
- */
- private java.util.Vector _colourList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewUserColours() {
- super();
- this._colourList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addColour(
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- this._colourList.addElement(vColour);
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addColour(
- final int index,
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- this._colourList.add(index, vColour);
- }
-
- /**
- * Method enumerateColour.
- *
- * @return an Enumeration over all Colour elements
- */
- public java.util.Enumeration enumerateColour(
- ) {
- return this._colourList.elements();
- }
-
- /**
- * Method getColour.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the Colour at the given index
- */
- public Colour getColour(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size()) {
- throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
- }
-
- return (Colour) _colourList.get(index);
- }
-
- /**
- * Method getColour.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public Colour[] getColour(
- ) {
- Colour[] array = new Colour[0];
- return (Colour[]) this._colourList.toArray(array);
- }
-
- /**
- * Method getColourCount.
- *
- * @return the size of this collection
- */
- public int getColourCount(
- ) {
- return this._colourList.size();
- }
-
- /**
- * Returns the value of field 'schemeName'.
- *
- * @return the value of field 'SchemeName'.
- */
- public java.lang.String getSchemeName(
- ) {
- return this._schemeName;
- }
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Jalview colour scheme
- * document version.
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllColour(
- ) {
- this._colourList.clear();
- }
-
- /**
- * Method removeColour.
- *
- * @param vColour
- * @return true if the object was removed from the collection.
- */
- public boolean removeColour(
- final Colour vColour) {
- boolean removed = _colourList.remove(vColour);
- return removed;
+public class JalviewUserColours implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewUserColours()
+ {
+ super();
+ this._colourList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour()
+ {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException("getColour: Index value '"
+ + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
- /**
- * Method removeColourAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Colour removeColourAt(
- final int index) {
- java.lang.Object obj = this._colourList.remove(index);
- return (Colour) obj;
+ return (Colour) _colourList.get(index);
+ }
+
+ /**
+ * Method getColour.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Colour[] getColour()
+ {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
+ */
+ public int getColourCount()
+ {
+ return this._colourList.size();
+ }
+
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName()
+ {
+ return this._schemeName;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setColour(
- final int index,
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size()) {
- throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
- }
-
- this._colourList.set(index, vColour);
+ public void removeAllColour()
+ {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(final Colour vColour)
+ {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(final int index)
+ {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException("setColour: Index value '"
+ + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
- /**
- *
- *
- * @param vColourArray
- */
- public void setColour(
- final Colour[] vColourArray) {
- //-- copy array
- _colourList.clear();
-
- for (int i = 0; i < vColourArray.length; i++) {
- this._colourList.add(vColourArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'schemeName'.
- *
- * @param schemeName the value of field 'schemeName'.
- */
- public void setSchemeName(
- final java.lang.String schemeName) {
- this._schemeName = schemeName;
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Jalview colour scheme document
- * version.
- *
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(final Colour[] vColourArray)
+ {
+ // -- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++)
+ {
+ this._colourList.add(vColourArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName
+ * the value of field 'schemeName'.
+ */
+ public void setSchemeName(final java.lang.String schemeName)
+ {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+ jalview.binding.JalviewUserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbentry implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _items.
- */
- private java.util.Vector _items;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Pdbentry() {
- super();
- this._items = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- this._items.addElement(vPdbentryItem);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- this._items.add(index, vPdbentryItem);
- }
-
- /**
- * Method enumeratePdbentryItem.
- *
- * @return an Enumeration over all jalview.binding.PdbentryItem
- * elements
- */
- public java.util.Enumeration enumeratePdbentryItem(
- ) {
- return this._items.elements();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Method getPdbentryItem.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.PdbentryItem at the
- * given index
- */
- public jalview.binding.PdbentryItem getPdbentryItem(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._items.size()) {
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
- }
-
- return (jalview.binding.PdbentryItem) _items.get(index);
- }
-
- /**
- * Method getPdbentryItem.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.PdbentryItem[] getPdbentryItem(
- ) {
- jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
- return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
- }
-
- /**
- * Method getPdbentryItemCount.
- *
- * @return the size of this collection
- */
- public int getPdbentryItemCount(
- ) {
- return this._items.size();
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllPdbentryItem(
- ) {
- this._items.clear();
- }
-
- /**
- * Method removePdbentryItem.
- *
- * @param vPdbentryItem
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem) {
- boolean removed = _items.remove(vPdbentryItem);
- return removed;
+public class Pdbentry implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Pdbentry()
+ {
+ super();
+ this._items = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all jalview.binding.PdbentryItem elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem()
+ {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.PdbentryItem at the given index
+ */
+ public jalview.binding.PdbentryItem getPdbentryItem(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size())
+ {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+ + index + "' not in range [0.." + (this._items.size() - 1)
+ + "]");
}
- /**
- * Method removePdbentryItemAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.PdbentryItem removePdbentryItemAt(
- final int index) {
- java.lang.Object obj = this._items.remove(index);
- return (jalview.binding.PdbentryItem) obj;
+ return (jalview.binding.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.PdbentryItem[] getPdbentryItem()
+ {
+ jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+ return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+ }
+
+ /**
+ * Method getPdbentryItemCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbentryItemCount()
+ {
+ return this._items.size();
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setId(
- final java.lang.String id) {
- this._id = id;
+ public void removeAllPdbentryItem()
+ {
+ this._items.clear();
+ }
+
+ /**
+ * Method removePdbentryItem.
+ *
+ * @param vPdbentryItem
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
+ {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.binding.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPdbentryItem(final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size())
+ {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+ + index + "' not in range [0.." + (this._items.size() - 1)
+ + "]");
}
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setPdbentryItem(
- final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._items.size()) {
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
- }
-
- this._items.set(index, vPdbentryItem);
- }
-
- /**
- *
- *
- * @param vPdbentryItemArray
- */
- public void setPdbentryItem(
- final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
- //-- copy array
- _items.clear();
-
- for (int i = 0; i < vPdbentryItemArray.length; i++) {
- this._items.add(vPdbentryItemArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.binding.PdbentryItem[] vPdbentryItemArray)
+ {
+ // -- copy array
+ _items.clear();
+
+ for (int i = 0; i < vPdbentryItemArray.length; i++)
+ {
+ this._items.add(vPdbentryItemArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+ jalview.binding.Pdbentry.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
*
* @version $Revision$ $Date$
*/
-public class PdbentryItem implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PdbentryItem() {
- super();
- this._propertyList = new java.util.Vector();
+public class PdbentryItem implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PdbentryItem()
+ {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.binding.Property elements
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Property at the given index
+ */
+ public jalview.binding.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ return (jalview.binding.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Property[] getProperty()
+ {
+ jalview.binding.Property[] array = new jalview.binding.Property[0];
+ return (jalview.binding.Property[]) this._propertyList.toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount()
+ {
+ return this._propertyList.size();
+ }
+
+ /**
*/
- public void addProperty(
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
+ public void removeAllProperty()
+ {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(final jalview.binding.Property vProperty)
+ {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Property removePropertyAt(final int index)
+ {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.binding.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all jalview.binding.Property
- * elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.elements();
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Property at the
- * given index
- */
- public jalview.binding.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (jalview.binding.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Property[] getProperty(
- ) {
- jalview.binding.Property[] array = new jalview.binding.Property[0];
- return (jalview.binding.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final jalview.binding.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (jalview.binding.Property) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final jalview.binding.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
- }
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(final jalview.binding.Property[] vPropertyArray)
+ {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++)
+ {
+ this._propertyList.add(vPropertyArray[i]);
}
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbids extends Pdbentry
-implements java.io.Serializable
+public class Pdbids extends Pdbentry implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Pdbids() {
- super();
- }
-
+ public Pdbids()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+ jalview.binding.Pdbids.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Property implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Property() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final java.lang.String value) {
- this._value = value;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Property
- */
- public static jalview.binding.Property unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Property()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final java.lang.String value)
+ {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Property
+ */
+ public static jalview.binding.Property unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Property) Unmarshaller.unmarshal(
+ jalview.binding.Property.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Sequence extends SequenceType
-implements java.io.Serializable
+public class Sequence extends SequenceType implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence() {
- super();
- }
-
+ public Sequence()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+ jalview.binding.Sequence.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSet implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _gapChar.
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned.
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
- * Field _sequenceList.
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList.
- */
- private java.util.Vector _annotationList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSet() {
- super();
- this._sequenceList = new java.util.Vector();
- this._annotationList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotation(
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationList.addElement(vAnnotation);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotation(
- final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationList.add(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequence(
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceList.addElement(vSequence);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequence(
- final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceList.add(index, vSequence);
- }
-
- /**
- */
- public void deleteAligned(
- ) {
- this._has_aligned= false;
- }
-
- /**
- * Method enumerateAnnotation.
- *
- * @return an Enumeration over all jalview.binding.Annotation
- * elements
- */
- public java.util.Enumeration enumerateAnnotation(
- ) {
- return this._annotationList.elements();
- }
-
- /**
- * Method enumerateSequence.
- *
- * @return an Enumeration over all jalview.binding.Sequence
- * elements
- */
- public java.util.Enumeration enumerateSequence(
- ) {
- return this._sequenceList.elements();
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean getAligned(
- ) {
- return this._aligned;
- }
-
- /**
- * Method getAnnotation.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Annotation at the
- * given index
- */
- public jalview.binding.Annotation getAnnotation(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size()) {
- throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
- }
-
- return (jalview.binding.Annotation) _annotationList.get(index);
- }
-
- /**
- * Method getAnnotation.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Annotation[] getAnnotation(
- ) {
- jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
- return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
- }
-
- /**
- * Method getAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationCount(
- ) {
- return this._annotationList.size();
- }
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return the value of field 'GapChar'.
- */
- public java.lang.String getGapChar(
- ) {
- return this._gapChar;
- }
-
- /**
- * Method getSequence.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.binding.Sequence at the
- * given index
- */
- public jalview.binding.Sequence getSequence(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size()) {
- throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
- }
-
- return (jalview.binding.Sequence) _sequenceList.get(index);
- }
-
- /**
- * Method getSequence.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Sequence[] getSequence(
- ) {
- jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
- return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
- }
-
- /**
- * Method getSequenceCount.
- *
- * @return the size of this collection
- */
- public int getSequenceCount(
- ) {
- return this._sequenceList.size();
- }
-
- /**
- * Method hasAligned.
- *
- * @return true if at least one Aligned has been added
- */
- public boolean hasAligned(
- ) {
- return this._has_aligned;
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean isAligned(
- ) {
- return this._aligned;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllAnnotation(
- ) {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence(
- ) {
- this._sequenceList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.binding.Annotation vAnnotation) {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Annotation removeAnnotationAt(
- final int index) {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.binding.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(
- final jalview.binding.Sequence vSequence) {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Sequence removeSequenceAt(
- final int index) {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.binding.Sequence) obj;
- }
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned the value of field 'aligned'.
- */
- public void setAligned(
- final boolean aligned) {
- this._aligned = aligned;
- this._has_aligned = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAnnotation(
- final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size()) {
- throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
- }
-
- this._annotationList.set(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vAnnotationArray
- */
- public void setAnnotation(
- final jalview.binding.Annotation[] vAnnotationArray) {
- //-- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++) {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(
- final java.lang.String gapChar) {
- this._gapChar = gapChar;
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequence(
- final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size()) {
- throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
- }
-
- this._sequenceList.set(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceArray
- */
- public void setSequence(
- final jalview.binding.Sequence[] vSequenceArray) {
- //-- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++) {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceSet
- */
- public static jalview.binding.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class SequenceSet implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned.
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSet()
+ {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ */
+ public void deleteAligned()
+ {
+ this._has_aligned = false;
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.binding.Annotation elements
+ */
+ public java.util.Enumeration enumerateAnnotation()
+ {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.binding.Sequence elements
+ */
+ public java.util.Enumeration enumerateSequence()
+ {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean getAligned()
+ {
+ return this._aligned;
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Annotation at the given index
+ */
+ public jalview.binding.Annotation getAnnotation(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size())
+ {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+ + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Annotation) _annotationList.get(index);
+ }
+
+ /**
+ * Method getAnnotation.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Annotation[] getAnnotation()
+ {
+ jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+ return (jalview.binding.Annotation[]) this._annotationList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationCount()
+ {
+ return this._annotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar()
+ {
+ return this._gapChar;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Sequence at the given index
+ */
+ public jalview.binding.Sequence getSequence(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Sequence) _sequenceList.get(index);
+ }
+
+ /**
+ * Method getSequence.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Sequence[] getSequence()
+ {
+ jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+ return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount()
+ {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method hasAligned.
+ *
+ * @return true if at least one Aligned has been added
+ */
+ public boolean hasAligned()
+ {
+ return this._has_aligned;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean isAligned()
+ {
+ return this._aligned;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotation()
+ {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence()
+ {
+ this._sequenceList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.binding.Annotation vAnnotation)
+ {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Annotation removeAnnotationAt(final int index)
+ {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.binding.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(final jalview.binding.Sequence vSequence)
+ {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Sequence removeSequenceAt(final int index)
+ {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.binding.Sequence) obj;
+ }
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned
+ * the value of field 'aligned'.
+ */
+ public void setAligned(final boolean aligned)
+ {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotation(final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size())
+ {
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+ + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
+ }
+
+ this._annotationList.set(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationArray
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation[] vAnnotationArray)
+ {
+ // -- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++)
+ {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar
+ * the value of field 'gapChar'.
+ */
+ public void setGapChar(final java.lang.String gapChar)
+ {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequence(final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(final jalview.binding.Sequence[] vSequenceArray)
+ {
+ // -- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++)
+ {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceSet
+ */
+ public static jalview.binding.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
+ jalview.binding.SequenceSet.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceType implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _sequence.
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public java.lang.String getSequence(
- ) {
- return this._sequence;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(
- final java.lang.String sequence) {
- this._sequence = sequence;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceType()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence()
+ {
+ return this._sequence;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence
+ * the value of field 'sequence'.
+ */
+ public void setSequence(final java.lang.String sequence)
+ {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+ jalview.binding.SequenceType.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Setting implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _display.
- */
- private boolean _display;
-
- /**
- * keeps track of state for field: _display
- */
- private boolean _has_display;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Setting() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deleteDisplay(
- ) {
- this._has_display= false;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean getDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
+public class Setting implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Setting()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasDisplay.
- *
- * @return true if at least one Display has been added
- */
- public boolean hasDisplay(
- ) {
- return this._has_display;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean isDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'display'.
- *
- * @param display the value of field 'display'.
- */
- public void setDisplay(
- final boolean display) {
- this._display = display;
- this._has_display = true;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Setting
- */
- public static jalview.binding.Setting unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
- }
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteDisplay()
+ {
+ this._has_display = false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay()
+ {
+ return this._has_display;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display
+ * the value of field 'display'.
+ */
+ public void setDisplay(final boolean display)
+ {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Setting
+ */
+ public static jalview.binding.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Setting) Unmarshaller.unmarshal(
+ jalview.binding.Setting.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Tree implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _showBootstrap.
- */
- private boolean _showBootstrap;
-
- /**
- * keeps track of state for field: _showBootstrap
- */
- private boolean _has_showBootstrap;
-
- /**
- * Field _showDistances.
- */
- private boolean _showDistances;
-
- /**
- * keeps track of state for field: _showDistances
- */
- private boolean _has_showDistances;
-
- /**
- * Field _markUnlinked.
- */
- private boolean _markUnlinked;
-
- /**
- * keeps track of state for field: _markUnlinked
- */
- private boolean _has_markUnlinked;
-
- /**
- * Field _fitToWindow.
- */
- private boolean _fitToWindow;
-
- /**
- * keeps track of state for field: _fitToWindow
- */
- private boolean _has_fitToWindow;
-
- /**
- * Field _currentTree.
- */
- private boolean _currentTree;
-
- /**
- * keeps track of state for field: _currentTree
- */
- private boolean _has_currentTree;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newick.
- */
- private java.lang.String _newick;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteCurrentTree(
- ) {
- this._has_currentTree= false;
- }
-
- /**
- */
- public void deleteFitToWindow(
- ) {
- this._has_fitToWindow= false;
- }
-
- /**
- */
- public void deleteFontSize(
- ) {
- this._has_fontSize= false;
- }
-
- /**
- */
- public void deleteFontStyle(
- ) {
- this._has_fontStyle= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteMarkUnlinked(
- ) {
- this._has_markUnlinked= false;
- }
-
- /**
- */
- public void deleteShowBootstrap(
- ) {
- this._has_showBootstrap= false;
- }
-
- /**
- */
- public void deleteShowDistances(
- ) {
- this._has_showDistances= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean getCurrentTree(
- ) {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean getFitToWindow(
- ) {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName(
- ) {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize(
- ) {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle(
- ) {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean getMarkUnlinked(
- ) {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return the value of field 'Newick'.
- */
- public java.lang.String getNewick(
- ) {
- return this._newick;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean getShowBootstrap(
- ) {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean getShowDistances(
- ) {
- return this._showDistances;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasCurrentTree.
- *
- * @return true if at least one CurrentTree has been added
- */
- public boolean hasCurrentTree(
- ) {
- return this._has_currentTree;
- }
-
- /**
- * Method hasFitToWindow.
- *
- * @return true if at least one FitToWindow has been added
- */
- public boolean hasFitToWindow(
- ) {
- return this._has_fitToWindow;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize(
- ) {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle(
- ) {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasMarkUnlinked.
- *
- * @return true if at least one MarkUnlinked has been added
- */
- public boolean hasMarkUnlinked(
- ) {
- return this._has_markUnlinked;
- }
-
- /**
- * Method hasShowBootstrap.
- *
- * @return true if at least one ShowBootstrap has been added
- */
- public boolean hasShowBootstrap(
- ) {
- return this._has_showBootstrap;
- }
-
- /**
- * Method hasShowDistances.
- *
- * @return true if at least one ShowDistances has been added
- */
- public boolean hasShowDistances(
- ) {
- return this._has_showDistances;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean isCurrentTree(
- ) {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean isFitToWindow(
- ) {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean isMarkUnlinked(
- ) {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean isShowBootstrap(
- ) {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean isShowDistances(
- ) {
- return this._showDistances;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'currentTree'.
- *
- * @param currentTree the value of field 'currentTree'.
- */
- public void setCurrentTree(
- final boolean currentTree) {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- }
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow the value of field 'fitToWindow'.
- */
- public void setFitToWindow(
- final boolean fitToWindow) {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(
- final java.lang.String fontName) {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(
- final int fontSize) {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(
- final int fontStyle) {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(
- final boolean markUnlinked) {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- }
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick the value of field 'newick'.
- */
- public void setNewick(
- final java.lang.String newick) {
- this._newick = newick;
- }
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(
- final boolean showBootstrap) {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- }
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances the value of field 'showDistances'.
- */
- public void setShowDistances(
- final boolean showDistances) {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Tree
- */
- public static jalview.binding.Tree unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Tree implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Tree()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteCurrentTree()
+ {
+ this._has_currentTree = false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow()
+ {
+ this._has_fitToWindow = false;
+ }
+
+ /**
+ */
+ public void deleteFontSize()
+ {
+ this._has_fontSize = false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle()
+ {
+ this._has_fontStyle = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked()
+ {
+ this._has_markUnlinked = false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap()
+ {
+ this._has_showBootstrap = false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances()
+ {
+ this._has_showDistances = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree()
+ {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow()
+ {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked()
+ {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick()
+ {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap()
+ {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances()
+ {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree()
+ {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow()
+ {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked()
+ {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap()
+ {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances()
+ {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree()
+ {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow()
+ {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked()
+ {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap()
+ {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances()
+ {
+ return this._showDistances;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree
+ * the value of field 'currentTree'.
+ */
+ public void setCurrentTree(final boolean currentTree)
+ {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow
+ * the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(final boolean fitToWindow)
+ {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked
+ * the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(final boolean markUnlinked)
+ {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick
+ * the value of field 'newick'.
+ */
+ public void setNewick(final java.lang.String newick)
+ {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap
+ * the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(final boolean showBootstrap)
+ {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances
+ * the value of field 'showDistances'.
+ */
+ public void setShowDistances(final boolean showDistances)
+ {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Tree
+ */
+ public static jalview.binding.Tree unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Tree) Unmarshaller.unmarshal(
+ jalview.binding.Tree.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColourScheme extends JalviewUserColours
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+ java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColourScheme() {
- super();
- }
-
+ public UserColourScheme()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+ jalview.binding.UserColourScheme.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _userColourScheme.
- */
- private jalview.binding.UserColourScheme _userColourScheme;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColours() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'userColourScheme'.
- *
- * @return the value of field 'UserColourScheme'.
- */
- public jalview.binding.UserColourScheme getUserColourScheme(
- ) {
- return this._userColourScheme;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'userColourScheme'.
- *
- * @param userColourScheme the value of field 'userColourScheme'
- */
- public void setUserColourScheme(
- final jalview.binding.UserColourScheme userColourScheme) {
- this._userColourScheme = userColourScheme;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.UserColours
- */
- public static jalview.binding.UserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _userColourScheme.
+ */
+ private jalview.binding.UserColourScheme _userColourScheme;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public UserColours()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'userColourScheme'.
+ *
+ * @return the value of field 'UserColourScheme'.
+ */
+ public jalview.binding.UserColourScheme getUserColourScheme()
+ {
+ return this._userColourScheme;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'userColourScheme'.
+ *
+ * @param userColourScheme
+ * the value of field 'userColourScheme'
+ */
+ public void setUserColourScheme(
+ final jalview.binding.UserColourScheme userColourScheme)
+ {
+ this._userColourScheme = userColourScheme;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.UserColours
+ */
+ public static jalview.binding.UserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(
+ jalview.binding.UserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VAMSAS implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _alignmentList.
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList.
- */
- private java.util.Vector _sequenceSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS() {
- super();
- this._alignmentList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- this._sequenceSetList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignment(
- final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentList.addElement(vAlignment);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignment(
- final int index,
- final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentList.add(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSet(
- final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetList.addElement(vSequenceSet);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSet(
- final int index,
- final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetList.add(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- * Method enumerateAlignment.
- *
- * @return an Enumeration over all Alignment elements
- */
- public java.util.Enumeration enumerateAlignment(
- ) {
- return this._alignmentList.elements();
- }
-
- /**
- * Method enumerateSequenceSet.
- *
- * @return an Enumeration over all SequenceSet elements
- */
- public java.util.Enumeration enumerateSequenceSet(
- ) {
- return this._sequenceSetList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
- }
-
- /**
- * Method getAlignment.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the Alignment at the given index
- */
- public Alignment getAlignment(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size()) {
- throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
- }
-
- return (Alignment) _alignmentList.get(index);
- }
-
- /**
- * Method getAlignment.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public Alignment[] getAlignment(
- ) {
- Alignment[] array = new Alignment[0];
- return (Alignment[]) this._alignmentList.toArray(array);
- }
-
- /**
- * Method getAlignmentCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentCount(
- ) {
- return this._alignmentList.size();
- }
-
- /**
- * Method getSequenceSet.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the SequenceSet at the given index
- */
- public SequenceSet getSequenceSet(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size()) {
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
- }
-
- return (SequenceSet) _sequenceSetList.get(index);
- }
-
- /**
- * Method getSequenceSet.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public SequenceSet[] getSequenceSet(
- ) {
- SequenceSet[] array = new SequenceSet[0];
- return (SequenceSet[]) this._sequenceSetList.toArray(array);
- }
-
- /**
- * Method getSequenceSetCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetCount(
- ) {
- return this._sequenceSetList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (java.lang.String) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getTree(
- ) {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlignment.
- *
- * @param vAlignment
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignment(
- final Alignment vAlignment) {
- boolean removed = _alignmentList.remove(vAlignment);
- return removed;
- }
-
- /**
- * Method removeAlignmentAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Alignment removeAlignmentAt(
- final int index) {
- java.lang.Object obj = this._alignmentList.remove(index);
- return (Alignment) obj;
- }
-
- /**
- */
- public void removeAllAlignment(
- ) {
- this._alignmentList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSet(
- ) {
- this._sequenceSetList.clear();
- }
-
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- * Method removeSequenceSet.
- *
- * @param vSequenceSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSet(
- final SequenceSet vSequenceSet) {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public SequenceSet removeSequenceSetAt(
- final int index) {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (SequenceSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final java.lang.String vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlignment(
- final int index,
- final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size()) {
- throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
- }
-
- this._alignmentList.set(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vAlignmentArray
- */
- public void setAlignment(
- final Alignment[] vAlignmentArray) {
- //-- copy array
- _alignmentList.clear();
-
- for (int i = 0; i < vAlignmentArray.length; i++) {
- this._alignmentList.add(vAlignmentArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequenceSet(
- final int index,
- final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size()) {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
- }
-
- this._sequenceSetList.set(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vSequenceSetArray
- */
- public void setSequenceSet(
- final SequenceSet[] vSequenceSetArray) {
- //-- copy array
- _sequenceSetList.clear();
-
- for (int i = 0; i < vSequenceSetArray.length; i++) {
- this._sequenceSetList.add(vSequenceSetArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTree(
- final int index,
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final java.lang.String[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class VAMSAS implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _alignmentList.
+ */
+ private java.util.Vector _alignmentList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VAMSAS()
+ {
+ super();
+ this._alignmentList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignment(final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alignmentList.addElement(vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignment(final int index, final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alignmentList.add(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSet(final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetList.addElement(vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetList.add(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index, final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateAlignment.
+ *
+ * @return an Enumeration over all Alignment elements
+ */
+ public java.util.Enumeration enumerateAlignment()
+ {
+ return this._alignmentList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSet.
+ *
+ * @return an Enumeration over all SequenceSet elements
+ */
+ public java.util.Enumeration enumerateSequenceSet()
+ {
+ return this._sequenceSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method getAlignment.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the Alignment at the given index
+ */
+ public Alignment getAlignment(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size())
+ {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '"
+ + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
+ }
+
+ return (Alignment) _alignmentList.get(index);
+ }
+
+ /**
+ * Method getAlignment.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Alignment[] getAlignment()
+ {
+ Alignment[] array = new Alignment[0];
+ return (Alignment[]) this._alignmentList.toArray(array);
+ }
+
+ /**
+ * Method getAlignmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentCount()
+ {
+ return this._alignmentList.size();
+ }
+
+ /**
+ * Method getSequenceSet.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the SequenceSet at the given index
+ */
+ public SequenceSet getSequenceSet(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ return (SequenceSet) _sequenceSetList.get(index);
+ }
+
+ /**
+ * Method getSequenceSet.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public SequenceSet[] getSequenceSet()
+ {
+ SequenceSet[] array = new SequenceSet[0];
+ return (SequenceSet[]) this._sequenceSetList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetCount()
+ {
+ return this._sequenceSetList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getTree()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount()
+ {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlignment.
+ *
+ * @param vAlignment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignment(final Alignment vAlignment)
+ {
+ boolean removed = _alignmentList.remove(vAlignment);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Alignment removeAlignmentAt(final int index)
+ {
+ java.lang.Object obj = this._alignmentList.remove(index);
+ return (Alignment) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignment()
+ {
+ this._alignmentList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSet()
+ {
+ this._sequenceSetList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(final SequenceSet vSequenceSet)
+ {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public SequenceSet removeSequenceSetAt(final int index)
+ {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (SequenceSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final java.lang.String vTree)
+ {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeTreeAt(final int index)
+ {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlignment(final int index, final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size())
+ {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '"
+ + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
+ }
+
+ this._alignmentList.set(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentArray
+ */
+ public void setAlignment(final Alignment[] vAlignmentArray)
+ {
+ // -- copy array
+ _alignmentList.clear();
+
+ for (int i = 0; i < vAlignmentArray.length; i++)
+ {
+ this._alignmentList.add(vAlignmentArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
+ {
+ // -- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++)
+ {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index, final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final java.lang.String[] vTreeArray)
+ {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++)
+ {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+ jalview.binding.VAMSAS.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VamsasModel extends VAMSAS
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VamsasModel() {
- super();
- }
-
+ public VamsasModel()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+ jalview.binding.VamsasModel.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
+public class Viewport implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _showConservation.
+ */
+ private boolean _showConservation;
+
+ /**
+ * keeps track of state for field: _showConservation
+ */
+ private boolean _has_showConservation;
+
+ /**
+ * Field _showQuality.
+ */
+ private boolean _showQuality;
+
+ /**
+ * keeps track of state for field: _showQuality
+ */
+ private boolean _has_showQuality;
+
+ /**
+ * Field _showIdentity.
+ */
+ private boolean _showIdentity;
+
+ /**
+ * keeps track of state for field: _showIdentity
+ */
+ private boolean _has_showIdentity;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Viewport()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Field _showText.
+ /**
*/
- private boolean _showText;
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
- /**
- * keeps track of state for field: _showText
+ /**
*/
- private boolean _has_showText;
+ public void deleteConservationSelected()
+ {
+ this._has_conservationSelected = false;
+ }
- /**
- * Field _showColourText.
+ /**
*/
- private boolean _showColourText;
+ public void deleteFontSize()
+ {
+ this._has_fontSize = false;
+ }
- /**
- * keeps track of state for field: _showColourText
+ /**
*/
- private boolean _has_showColourText;
+ public void deleteFontStyle()
+ {
+ this._has_fontStyle = false;
+ }
- /**
- * Field _showBoxes.
+ /**
*/
- private boolean _showBoxes;
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
- /**
- * keeps track of state for field: _showBoxes
+ /**
*/
- private boolean _has_showBoxes;
+ public void deletePidSelected()
+ {
+ this._has_pidSelected = false;
+ }
- /**
- * Field _wrapAlignment.
+ /**
*/
- private boolean _wrapAlignment;
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
- /**
- * keeps track of state for field: _wrapAlignment
+ /**
*/
- private boolean _has_wrapAlignment;
+ public void deleteRenderGaps()
+ {
+ this._has_renderGaps = false;
+ }
- /**
- * Field _renderGaps.
+ /**
*/
- private boolean _renderGaps;
+ public void deleteShowAnnotation()
+ {
+ this._has_showAnnotation = false;
+ }
- /**
- * keeps track of state for field: _renderGaps
+ /**
*/
- private boolean _has_renderGaps;
+ public void deleteShowBoxes()
+ {
+ this._has_showBoxes = false;
+ }
- /**
- * Field _showSequenceFeatures.
+ /**
*/
- private boolean _showSequenceFeatures;
+ public void deleteShowColourText()
+ {
+ this._has_showColourText = false;
+ }
- /**
- * keeps track of state for field: _showSequenceFeatures
+ /**
*/
- private boolean _has_showSequenceFeatures;
+ public void deleteShowConservation()
+ {
+ this._has_showConservation = false;
+ }
- /**
- * Field _showAnnotation.
+ /**
*/
- private boolean _showAnnotation;
+ public void deleteShowFullId()
+ {
+ this._has_showFullId = false;
+ }
- /**
- * keeps track of state for field: _showAnnotation
+ /**
*/
- private boolean _has_showAnnotation;
+ public void deleteShowIdentity()
+ {
+ this._has_showIdentity = false;
+ }
- /**
- * Field _showConservation.
+ /**
*/
- private boolean _showConservation;
-
- /**
- * keeps track of state for field: _showConservation
- */
- private boolean _has_showConservation;
-
- /**
- * Field _showQuality.
- */
- private boolean _showQuality;
-
- /**
- * keeps track of state for field: _showQuality
- */
- private boolean _has_showQuality;
-
- /**
- * Field _showIdentity.
- */
- private boolean _showIdentity;
-
- /**
- * keeps track of state for field: _showIdentity
- */
- private boolean _has_showIdentity;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Viewport() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteConservationSelected(
- ) {
- this._has_conservationSelected= false;
- }
-
- /**
- */
- public void deleteFontSize(
- ) {
- this._has_fontSize= false;
- }
-
- /**
- */
- public void deleteFontStyle(
- ) {
- this._has_fontStyle= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deletePidSelected(
- ) {
- this._has_pidSelected= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteRenderGaps(
- ) {
- this._has_renderGaps= false;
- }
-
- /**
- */
- public void deleteShowAnnotation(
- ) {
- this._has_showAnnotation= false;
- }
-
- /**
- */
- public void deleteShowBoxes(
- ) {
- this._has_showBoxes= false;
- }
-
- /**
- */
- public void deleteShowColourText(
- ) {
- this._has_showColourText= false;
- }
-
- /**
- */
- public void deleteShowConservation(
- ) {
- this._has_showConservation= false;
- }
-
- /**
- */
- public void deleteShowFullId(
- ) {
- this._has_showFullId= false;
- }
-
- /**
- */
- public void deleteShowIdentity(
- ) {
- this._has_showIdentity= false;
- }
-
- /**
- */
- public void deleteShowQuality(
- ) {
- this._has_showQuality= false;
- }
-
- /**
- */
- public void deleteShowSequenceFeatures(
- ) {
- this._has_showSequenceFeatures= false;
- }
-
- /**
- */
- public void deleteShowText(
- ) {
- this._has_showText= false;
- }
-
- /**
- */
- public void deleteStartRes(
- ) {
- this._has_startRes= false;
- }
-
- /**
- */
- public void deleteStartSeq(
- ) {
- this._has_startSeq= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteWrapAlignment(
- ) {
- this._has_wrapAlignment= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour(
- ) {
- return this._bgColour;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName(
- ) {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize(
- ) {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle(
- ) {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean getShowConservation(
- ) {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean getShowIdentity(
- ) {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean getShowQuality(
- ) {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes(
- ) {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq(
- ) {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been
- * added
- */
- public boolean hasConservationSelected(
- ) {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize(
- ) {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle(
- ) {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected(
- ) {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps(
- ) {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation(
- ) {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes(
- ) {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText(
- ) {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConservation.
- *
- * @return true if at least one ShowConservation has been added
- */
- public boolean hasShowConservation(
- ) {
- return this._has_showConservation;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId(
- ) {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowIdentity.
- *
- * @return true if at least one ShowIdentity has been added
- */
- public boolean hasShowIdentity(
- ) {
- return this._has_showIdentity;
- }
-
- /**
- * Method hasShowQuality.
- *
- * @return true if at least one ShowQuality has been added
- */
- public boolean hasShowQuality(
- ) {
- return this._has_showQuality;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been
- * added
- */
- public boolean hasShowSequenceFeatures(
- ) {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText(
- ) {
- return this._has_showText;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes(
- ) {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq(
- ) {
- return this._has_startSeq;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment(
- ) {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean isShowConservation(
- ) {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean isShowIdentity(
- ) {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean isShowQuality(
- ) {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour the value of field 'bgColour'.
- */
- public void setBgColour(
- final java.lang.String bgColour) {
- this._bgColour = bgColour;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected the value of field
- * 'conservationSelected'.
- */
- public void setConservationSelected(
- final boolean conservationSelected) {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(
- final java.lang.String fontName) {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(
- final int fontSize) {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(
- final int fontStyle) {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected the value of field 'pidSelected'.
- */
- public void setPidSelected(
- final boolean pidSelected) {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps the value of field 'renderGaps'.
- */
- public void setRenderGaps(
- final boolean renderGaps) {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(
- final boolean showAnnotation) {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes the value of field 'showBoxes'.
- */
- public void setShowBoxes(
- final boolean showBoxes) {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText the value of field 'showColourText'.
- */
- public void setShowColourText(
- final boolean showColourText) {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConservation'.
- *
- * @param showConservation the value of field 'showConservation'
- */
- public void setShowConservation(
- final boolean showConservation) {
- this._showConservation = showConservation;
- this._has_showConservation = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId the value of field 'showFullId'.
- */
- public void setShowFullId(
- final boolean showFullId) {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showIdentity'.
- *
- * @param showIdentity the value of field 'showIdentity'.
- */
- public void setShowIdentity(
- final boolean showIdentity) {
- this._showIdentity = showIdentity;
- this._has_showIdentity = true;
- }
-
- /**
- * Sets the value of field 'showQuality'.
- *
- * @param showQuality the value of field 'showQuality'.
- */
- public void setShowQuality(
- final boolean showQuality) {
- this._showQuality = showQuality;
- this._has_showQuality = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures the value of field
- * 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(
- final boolean showSequenceFeatures) {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText the value of field 'showText'.
- */
- public void setShowText(
- final boolean showText) {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes the value of field 'startRes'.
- */
- public void setStartRes(
- final int startRes) {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq the value of field 'startSeq'.
- */
- public void setStartSeq(
- final int startSeq) {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(
- final boolean wrapAlignment) {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Viewport
- */
- public static jalview.binding.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ public void deleteShowQuality()
+ {
+ this._has_showQuality = false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures()
+ {
+ this._has_showSequenceFeatures = false;
+ }
+
+ /**
+ */
+ public void deleteShowText()
+ {
+ this._has_showText = false;
+ }
+
+ /**
+ */
+ public void deleteStartRes()
+ {
+ this._has_startRes = false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq()
+ {
+ this._has_startSeq = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment()
+ {
+ this._has_wrapAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour()
+ {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean getShowConservation()
+ {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean getShowIdentity()
+ {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean getShowQuality()
+ {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes()
+ {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq()
+ {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been added
+ */
+ public boolean hasConservationSelected()
+ {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected()
+ {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps()
+ {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation()
+ {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes()
+ {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText()
+ {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConservation.
+ *
+ * @return true if at least one ShowConservation has been added
+ */
+ public boolean hasShowConservation()
+ {
+ return this._has_showConservation;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId()
+ {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowIdentity.
+ *
+ * @return true if at least one ShowIdentity has been added
+ */
+ public boolean hasShowIdentity()
+ {
+ return this._has_showIdentity;
+ }
+
+ /**
+ * Method hasShowQuality.
+ *
+ * @return true if at least one ShowQuality has been added
+ */
+ public boolean hasShowQuality()
+ {
+ return this._has_showQuality;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been added
+ */
+ public boolean hasShowSequenceFeatures()
+ {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText()
+ {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes()
+ {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq()
+ {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment()
+ {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean isShowConservation()
+ {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean isShowIdentity()
+ {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean isShowQuality()
+ {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final java.lang.String bgColour)
+ {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected
+ * the value of field 'conservationSelected'.
+ */
+ public void setConservationSelected(final boolean conservationSelected)
+ {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected
+ * the value of field 'pidSelected'.
+ */
+ public void setPidSelected(final boolean pidSelected)
+ {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps
+ * the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(final boolean renderGaps)
+ {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation
+ * the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(final boolean showAnnotation)
+ {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes
+ * the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(final boolean showBoxes)
+ {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText
+ * the value of field 'showColourText'.
+ */
+ public void setShowColourText(final boolean showColourText)
+ {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConservation'.
+ *
+ * @param showConservation
+ * the value of field 'showConservation'
+ */
+ public void setShowConservation(final boolean showConservation)
+ {
+ this._showConservation = showConservation;
+ this._has_showConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId
+ * the value of field 'showFullId'.
+ */
+ public void setShowFullId(final boolean showFullId)
+ {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showIdentity'.
+ *
+ * @param showIdentity
+ * the value of field 'showIdentity'.
+ */
+ public void setShowIdentity(final boolean showIdentity)
+ {
+ this._showIdentity = showIdentity;
+ this._has_showIdentity = true;
+ }
+
+ /**
+ * Sets the value of field 'showQuality'.
+ *
+ * @param showQuality
+ * the value of field 'showQuality'.
+ */
+ public void setShowQuality(final boolean showQuality)
+ {
+ this._showQuality = showQuality;
+ this._has_showQuality = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures
+ * the value of field 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+ {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText
+ * the value of field 'showText'.
+ */
+ public void setShowText(final boolean showText)
+ {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes
+ * the value of field 'startRes'.
+ */
+ public void setStartRes(final int startRes)
+ {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq
+ * the value of field 'startSeq'.
+ */
+ public void setStartSeq(final int startSeq)
+ {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment
+ * the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(final boolean wrapAlignment)
+ {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Viewport
+ */
+ public static jalview.binding.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(
+ jalview.binding.Viewport.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
* @param performEdit
*/
final public void appendEdit(Action command, SequenceI[] seqs,
- int position,
- int number, AlignmentI al, boolean performEdit)
+ int position, int number, AlignmentI al, boolean performEdit)
{
appendEdit(command, seqs, position, number, al, performEdit, null);
}
* @param views
*/
final public void appendEdit(Action command, SequenceI[] seqs,
- int position,
- int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
+ int position, int number, AlignmentI al, boolean performEdit,
+ AlignmentI[] views)
{
Edit edit = new Edit(command, seqs, position, number,
al.getGapCharacter());
*/
@Override
final public void undoCommand(AlignmentI[] views)
- {
+ {
ListIterator<Edit> iterator = edits.listIterator(edits.size());
while (iterator.hasPrevious())
{
for (int s = 0; s < command.seqs.length; s++)
{
- command.seqs[s].insertCharAt(command.position,
- command.number, command.gapChar);
+ command.seqs[s].insertCharAt(command.position, command.number,
+ command.gapChar);
// System.out.println("pos: "+command.position+" number: "+command.number);
}
command,
i,
sequence.findPosition(command.position),
- sequence.findPosition(command.position
- + command.number), false);
+ sequence.findPosition(command.position + command.number),
+ false);
}
}
}
int copylen = Math.min(command.position,
annotations[a].annotations.length);
if (copylen > 0)
- {
+ {
System.arraycopy(annotations[a].annotations, 0, temp, 0,
copylen); // command.position);
}
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence.setSequenceFeatures(command.editedFeatures
- .get(seq));
+ sequence.setSequenceFeatures(command.editedFeatures.get(seq));
}
return;
if (action == Action.DELETE_GAP)
{
preEdit.setSequence(new String(StringUtils.insertCharAt(
- preEdit.getSequence(), position,
- number, gap)));
+ preEdit.getSequence(), position, number, gap)));
}
else if (action == Action.INSERT_GAP)
{
if (!delete && startCol > -1)
{
this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
- endCol
- - startCol, al, false, null);
+ endCol - startCol, al, false, null);
columnsDeleted += (endCol - startCol);
startCol = -1;
// end of the alignment
this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
- end
- - startCol + 1, al, false, null);
+ end - startCol + 1, al, false, null);
columnsDeleted += (end - startCol + 1);
}
if (!delete && startCol > -1)
{
- this.appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
- al, false, null);
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+ start + startCol - deletedCols, endCol - startCol, al,
+ false, null);
deletedCols += (endCol - startCol);
startCol = -1;
}
if (delete && startCol > -1)
{
- this.appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+ start + startCol - deletedCols, jSize - startCol, al,
false, null);
}
if (sg != null
&& (cs == null || cs.getSelected() == null || cs.size() == 0))
{
- gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- } else {
- if (cs!=null) {
+ gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
+ .getSequenceSelection(), viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()), viewport
+ .getAlignment().getGroups());
+ }
+ else
+ {
+ if (cs != null)
+ {
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
: sg.getSequences().toArray(new SequenceI[0]), cs,
viewport.getAlignment().getGroups());
}
}
- if (gps!=null) {
+ if (gps != null)
+ {
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
}
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
- new String[]{
- (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString()
- }));
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ (toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked")),
+ (invert ? (Integer.valueOf((alw - alStart)
+ - bs.cardinality()).toString()) : (Integer
+ .valueOf(bs.cardinality()).toString())),
+ featureType, Integer.valueOf(nseq).toString() }));
return true;
}
else
{
- avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
if (!extendCurrent && cs != null)
{
cs.clear();
}
}
-
-
@Override
public void sortAlignmentByFeatureDensity(String[] typ)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
if (typ == null)
{
- typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+ typ = fr == null ? null : fr.getDisplayedFeatureTypes();
}
String gps[] = null;
- gps = fr==null ? null : fr.getDisplayedFeatureGroups();
+ gps = fr == null ? null : fr.getDisplayedFeatureGroups();
if (typ != null)
{
ArrayList types = new ArrayList();
import jalview.api.FeatureSettingsModelI;
public class FeatureSettingsController // implements
- // jalview.api.FeatureSettingsControllerI
+// jalview.api.FeatureSettingsControllerI
{
FeatureSettingsControllerGuiI settingUI;
+
FeatureRenderer fr;
+
FeatureSettingsModelI fsettings;
-
+
}
*/
package jalview.datamodel;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
if (dnaSeqs[mi] == targetDs && dnaToProt[mi].to == sourceDs)
{
int[] codon = dnaToProt[mi].map.locateInFrom(pos, pos);
- if (codon != null) {
+ if (codon != null)
+ {
return codon;
}
}
* Read off the mapped nucleotides (converting to position base 0)
*/
codonPos = MappingUtils.flattenRanges(codonPos);
- return new char[]
- { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
+ return new char[] { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
dnaSeq[codonPos[2] - 1] };
}
List<SequenceI> related = new ArrayList<SequenceI>();
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
-
+
for (int ds = 0; ds < dnaSeqs.length; ds++)
{
final Mapping mapping = dnaToProt[ds];
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
+ throw new Error(
+ MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
}
if (sequences == null)
{
- initAlignment(new SequenceI[]
- { snew });
+ initAlignment(new SequenceI[] { snew });
}
else
{
}
}
+ private SequenceI seqrep = null;
- private SequenceI seqrep=null;
-
- /**
- *
- * @return the representative sequence for this group
- */
- public SequenceI getSeqrep()
- {
- return seqrep;
- }
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
- /**
- * set the representative sequence for this group. Note - this affects the
- * interpretation of the Hidereps attribute.
- *
- * @param seqrep
- * the seqrep to set (null means no sequence representative)
- */
- public void setSeqrep(SequenceI seqrep)
- {
- this.seqrep = seqrep;
- }
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
- /**
- *
- * @return true if group has a sequence representative
- */
- public boolean hasSeqrep()
- {
- return seqrep != null;
- }
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
@Override
public int getEndRes()
* @param preserveUnmappedGaps
* if true, gaps within and between unmapped codons are preserved
*/
-// @Override
+ // @Override
public int alignAs(AlignmentI al, boolean preserveMappedGaps,
boolean preserveUnmappedGaps)
{
char thisGapChar = this.getGapCharacter();
String gap = thisIsNucleotide && thatIsProtein ? String
- .valueOf(new char[]
- { thisGapChar, thisGapChar, thisGapChar }) : String
- .valueOf(thisGapChar);
+ .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+ : String.valueOf(thisGapChar);
// TODO handle intron regions? Needs a 'holistic' alignment of dna,
// not just sequence by sequence. But how to 'gap' intron regions?
*/
for (SequenceI alignTo : getSequences())
{
- count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps,
- preserveUnmappedGaps) ? 1 : 0;
+ count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+ preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
}
return count;
}
*/
package jalview.datamodel;
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Map;
import java.util.Map.Entry;
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
/**
* DOCUMENT ME!
*
}
setScore(mxval);
}
+
/**
* map of positions in the associated annotation
*/
this.scaleColLabel = annotation.scaleColLabel;
this.showAllColLabels = annotation.showAllColLabels;
this.calcId = annotation.calcId;
- if (annotation.properties!=null)
+ if (annotation.properties != null)
{
- properties = new HashMap<String,String>();
- for (Map.Entry<String, String> val:annotation.properties.entrySet())
+ properties = new HashMap<String, String>();
+ for (Map.Entry<String, String> val : annotation.properties.entrySet())
{
properties.put(val.getKey(), val.getValue());
}
{
if (sequenceRef != null)
{
- boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null;
+ boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
+ .getDatasetSequence() == null;
if (sequenceRef != sequenceI
&& (rIsDs && !tIsDs && sequenceRef != sequenceI
.getDatasetSequence())
{
if (sp2sq.getMappedWidth() != sp2sq.getWidth())
{
- // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
- throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+ // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+ // Protein reference frames
+ throw new Error(
+ "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
}
boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
.getTo() == sq.getDatasetSequence()) : false;
public void setProperty(String property, String value)
{
- if (properties==null)
+ if (properties == null)
{
- properties = new HashMap<String,String>();
+ properties = new HashMap<String, String>();
}
properties.put(property, value);
}
import jalview.api.AlignExportSettingI;
-
public class AlignmentExportData
{
private AlignmentI alignment;
*
* @return existing annotation matching the given attributes
*/
- AlignmentAnnotation findOrCreateAnnotation(String name,
- String calcId, boolean autoCalc, SequenceI seqRef,
- SequenceGroup groupRef);
+ AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
/**
* move the given group up or down in the alignment by the given number of
* one or more ScGroup objects, which are referenced by each seqCigar's group
* membership
*/
- private List<ScGroup> scGroups=null;
+ private List<ScGroup> scGroups = null;
private boolean isNa = false;
selseqs = alignment.getSequencesArray();
}
- List<List<SequenceI>> seqsets=new ArrayList<List<SequenceI>>();
+ List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
// get the alignment's group list and make a copy
List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
List<SequenceGroup> gg = alignment.getGroups();
{
if (!seqcigararray.isSeqCigarArray())
{
- throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
{
ColumnSelection colsel = new ColumnSelection();
- return new Object[]
- {
+ return new Object[] {
SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
contigs), colsel };
}
{
if (sequences == null || width <= 0)
{
- throw new Error(MessageManager.getString("error.empty_view_cannot_be_updated"));
+ throw new Error(
+ MessageManager
+ .getString("error.empty_view_cannot_be_updated"));
}
if (nvismsa == null)
{
j++;
if (mseq.length != sequences.length)
{
- throw new Error(MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(mseq.length).toString(),Integer.valueOf(sequences.length).toString() }));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.mismatch_between_number_of_sequences_in_block",
+ new String[] {
+ Integer.valueOf(j).toString(),
+ Integer.valueOf(mseq.length)
+ .toString(),
+ Integer.valueOf(
+ sequences.length)
+ .toString() }));
}
swidth = mseq[0].getLength(); // JBPNote: could ensure padded
// here.
else
{
// place gaps.
- throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
+ throw new Error(
+ MessageManager
+ .getString("error.padding_not_yet_implemented"));
}
}
}
}
}
- return new Object[]
- { alignment, columnselection };
+ return new Object[] { alignment, columnselection };
}
else
{
if (nvismsa.length != 1)
{
- throw new Error(MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", new String[]{Integer.valueOf(nvismsa.length).toString()}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+ new String[] { Integer.valueOf(
+ nvismsa.length).toString() }));
}
if (nvismsa[0] != null)
{
- return new Object[]
- { nvismsa[0], new ColumnSelection() };
+ return new Object[] { nvismsa[0], new ColumnSelection() };
}
else
{
}
else
{
- return new int[]
- { 0, width };
+ return new int[] { 0, width };
}
}
*/
package jalview.datamodel;
-import jalview.schemes.*;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
/**
* Encode a sequence as a numeric vector using either classic residue binary
private static int[] _calcStartEndBounds(AlignmentI alignment,
SequenceGroup selectionGroup)
{
- int[] startend = new int[]
- { 0, 0, 0 };
+ int[] startend = new int[] { 0, 0, 0 };
if (selectionGroup != null)
{
startend[0] = selectionGroup.getSize();
delpos = new java.util.Vector();
}
int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
- delpos.addElement(new int[]
- { vcursor + offset, range[i] }); // index of right hand column after
+ delpos.addElement(new int[] { vcursor + offset, range[i] }); // index of
+ // right
+ // hand
+ // column
+ // after
// hidden region boundary
offset += range[i] - 1; // shift in visible column coordinates
System.arraycopy(operation, i + 1, operation, i, length - i);
import jalview.util.MessageManager;
-import java.util.*;
+import java.util.Vector;
public abstract class CigarBase
{
case D:
if (!consecutive_del)
{
- deletions[++delcount] = new int[]
- { cursor, 0, alcursor };
+ deletions[++delcount] = new int[] { cursor, 0, alcursor };
}
cursor += range[i];
deletions[delcount][1] = cursor - 1;
endpos = alcursor;
break;
default:
- throw new Error(MessageManager.formatMessage("error.unknown_seq_cigar_operation", new String[]{new StringBuffer(operation[i]).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.unknown_seq_cigar_operation",
+ new String[] { new StringBuffer(operation[i]).toString() }));
}
}
if (++delcount > 0)
System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
}
deletions = null;
- return new Object[]
- { ((reference != null) ? sq.toString() : null), new int[]
- { start, startpos, end, endpos }, trunc_deletions };
+ return new Object[] { ((reference != null) ? sq.toString() : null),
+ new int[] { start, startpos, end, endpos }, trunc_deletions };
}
protected void compact_operations()
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
- throw new Exception(MessageManager.getString("exception.unterminated_cigar_string"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.unterminated_cigar_string"));
}
try
{
i = j;
} catch (Exception e)
{
- throw new Error(MessageManager.getString("error.implementation_bug_parse_cigar_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_bug_parse_cigar_string"));
}
if (c >= 'a' && c <= 'z')
{
}
else
{
- throw new Exception(MessageManager.formatMessage("exception.unexpected_operation_cigar_string_pos", new String[]{
- new StringBuffer(c).toString(),
- Integer.valueOf(i).toString(),
- cigarString
- }));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.unexpected_operation_cigar_string_pos",
+ new String[] { new StringBuffer(c).toString(),
+ Integer.valueOf(i).toString(), cigarString }));
}
}
- return new Object[]
- { operation, range };
+ return new Object[] { operation, range };
}
/**
}
if (op != M && op != D && op != I)
{
- throw new Error(MessageManager.getString("error.implementation_error_invalid_operation_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_invalid_operation_string"));
}
if (range == 0)
{
}
if (range < 0)
{
- throw new Error(MessageManager.getString("error.invalid_range_string"));
+ throw new Error(
+ MessageManager.getString("error.invalid_range_string"));
}
int lngth = 0;
if (operation == null)
}
if (start < 0 || start > end)
{
- throw new Error(MessageManager.getString("error.implementation_error_delete_range_out_of_bounds"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_delete_range_out_of_bounds"));
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
}
break;
case D:
- throw new Error(MessageManager.getString("error.implementation_error")); // do nothing;
+ throw new Error(
+ MessageManager.getString("error.implementation_error")); // do
+ // nothing;
default:
- throw new Error(MessageManager.formatMessage("error.implementation_error_unknown_operation", new String[]{new StringBuffer(oldops[o]).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_unknown_operation",
+ new String[] { new StringBuffer(oldops[o]).toString() }));
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
vcursor += range[i];
break;
case D:
- dr.addElement(new int[]
- { vcursor, cursor, range[i] });
+ dr.addElement(new int[] { vcursor, cursor, range[i] });
cursor += range[i];
}
}
/**
* This Method is used to return all the HiddenColumn regions
+ *
* @return empty list or List of hidden column intervals
*/
public List<int[]> getHiddenColumns()
}
else if (end < region[0] && start < region[0])
{
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
added = true;
break;
}
}
else if (!added)
{
- hiddenColumns.addElement(new int[]
- { start, end });
+ hiddenColumns.addElement(new int[] { start, end });
}
}
}
if (hideStart > vstart)
{
- visiblecontigs.add(new int[]
- { vstart, hideStart - 1 });
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
- visiblecontigs.add(new int[]
- { vstart, end - 1 });
+ visiblecontigs.add(new int[] { vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
}
else
{
- return new int[]
- { start, end - 1 };
+ return new int[] { start, end - 1 };
}
}
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector<Annotation []> annels = new Vector<Annotation []>();
+ Vector<Annotation[]> annels = new Vector<Annotation[]>();
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- for (Annotation [] chnk : annels)
+ for (Annotation[] chnk : annels)
{
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
{
return hiddenColumns != null && hiddenColumns.size() > 0;
}
-
+
/**
*
* @return true if there are more than one set of columns hidden
hideColumns(r[0], r[1]);
}
}
-
+
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
-
+
public static final String EMBLCDSProduct = "EMBLCDSProtein"
.toUpperCase();
/**
* List of databases whose sequences might have coding regions annotated
*/
- public static final String[] DNACODINGDBS =
- { EMBL, EMBLCDS, GENEDB };
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
- public static final String[] CODINGDBS =
- { EMBLCDS, GENEDB };
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
- public static final String[] PROTEINDBS =
- { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct };
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct };
- public static final String[] PROTEINSEQ =
- { UNIPROT, UNIPROTKB, EMBLCDSProduct };
+ public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct };
- public static final String[] PROTEINSTR =
- { PDB };
+ public static final String[] PROTEINSTR = { PDB };
- public static final String[] DOMAINDBS =
- { PFAM, RFAM };
+ public static final String[] DOMAINDBS = { PFAM, RFAM };
/**
* set of unique DBRefSource property constants. These could be used to
*/
package jalview.datamodel;
+import jalview.util.MapList;
+
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
-import jalview.util.MapList;
-
public class Mapping
{
/**
{
// TODO should ideally handle toRatio other than 1 as well...
// i.e. code like getNextCodon()
- if (toPosition <= currentToRange[1]) {
+ if (toPosition <= currentToRange[1])
+ {
char pep = Mapping.this.to.getSequence()[toPosition - 1];
toPosition++;
return String.valueOf(pep);
int[] mp = map.shiftFrom(pos);
if (mp != null)
{
- return new int[]
- { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
+ return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
}
}
return null;
}
}
// give up and just return the feature.
- return new SequenceFeature[]
- { f };
+ return new SequenceFeature[] { f };
}
/**
}
return map.locateInFrom(from, to);
}
- return new int[]
- { from, to };
+ return new int[] { from, to };
}
/**
}
return map.locateInTo(from, to);
}
- return new int[]
- { from, to };
+ return new int[] { from, to };
}
/**
{
for (int m = 0; m < mpr.length; m += 2)
{
- toRange.addElement(new int[]
- { mpr[m], mpr[m + 1] });
+ toRange.addElement(new int[] { mpr[m], mpr[m + 1] });
int[] xpos = locateRange(mpr[m], mpr[m + 1]);
for (int x = 0; x < xpos.length; x += 2)
{
- fromRange.addElement(new int[]
- { xpos[x], xpos[x + 1] });
+ fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
}
}
}
{
PDB, FILE
}
+
Hashtable properties;
/*
return true;
}
PDBEntry o = (PDBEntry) obj;
- return
- (type == o.type || (type != null && o.type != null && o.type
- .equals(type)))
+ return (type == o.type || (type != null && o.type != null && o.type
+ .equals(type)))
&& (id == o.id || (id != null && o.id != null && o.id
.equalsIgnoreCase(id)))
&& (chainCode == o.chainCode || (chainCode != null
&& (properties == o.properties || (properties != null
&& o.properties != null && properties
.equals(o.properties)));
-
+
}
/**
// this.file = filePath;
// this.id = pdbId;
// }
-
+
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
{
this.type = t;
}
+
public void setType(PDBEntry.Type type)
{
this.type = type == null ? null : type.toString();
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Vector;
public class Provenance
{
package jalview.datamodel;
-
/**
* A data bean class to hold properties of an RNA viewer
*/
* @param dividerLocation
*/
public RnaViewerModel(String viewId, String title, int xpos, int ypos,
- int width,
- int height, int dividerLocation)
+ int width, int height, int dividerLocation)
{
this.viewId = viewId;
this.title = title;
if (result == null)
{
- result = new int[]
- { matchStart, matchEnd };
+ result = new int[] { matchStart, matchEnd };
}
else
{
*/
package jalview.datamodel;
-import java.util.Enumeration;
-import java.util.Hashtable;
-
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
public class SeqCigar extends CigarSimple
{
/**
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
}
int bounds[] = (int[]) edit_result[1];
seq = new Sequence(refseq.getName(), (String) edit_result[0],
boolean hasgaps = false;
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_s", new String[] { Integer
+ .valueOf(_s).toString() }));
}
String seq_string = seq.getSequenceAsString();
if (_e == 0 || _e < _s || _e > seq_string.length())
// Check offsets
if (end > ds.getLength())
{
- throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
+ throw new Error(
+ MessageManager.getString("error.implmentation_bug_seq_null"));
}
if (operation.length != range.length)
{
- throw new Error(MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_bug_cigar_operation_list_range_list"));
}
if (operation != null)
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
for (int i = this.length, j = 0; j < operation.length; i++, j++)
{
char op = operation[j];
if (op != M && op != I && op != D)
{
- throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_bug_cigar_operation", new String[] {
+ Integer.valueOf(j).toString(),
+ Integer.valueOf(op).toString(),
+ Integer.valueOf(M).toString(),
+ Integer.valueOf(I).toString(),
+ Integer.valueOf(D).toString() }));
}
this.operation[i] = op;
this.range[i] = range[j];
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
// endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cigar_seq_no_operations",
+ new String[] { Integer.valueOf(i).toString() }));
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
// visible
RNA rna;
-
/**
* This annotation is displayed below the alignment but the positions are tied
* to the residues of this sequence
{
if (lastj != -1)
{
- map.add(new int[]
- { lastj, j - 1 });
+ map.add(new int[] { lastj, j - 1 });
lastj = -1;
}
}
}
if (lastj != -1)
{
- map.add(new int[]
- { lastj, j - 1 });
+ map.add(new int[] { lastj, j - 1 });
lastj = -1;
}
return map;
.toArray(new AlignmentAnnotation[annotation.size()]);
}
-
@Override
public boolean hasAnnotation(AlignmentAnnotation ann)
{
for (int si = 0; si < sfs.length; si++)
{
SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
- : new SequenceFeature[]
- { new SequenceFeature(sfs[si]) };
+ : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
if (sf != null && sf.length > 0)
{
for (int sfi = 0; sfi < sf.length; sfi++)
List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
+
int getWidth();
+
/**
*
* @return true if getSeqrep doesn't return null
*/
boolean hasSeqrep();
+
/**
* get the reference or representative sequence within this collection
+ *
* @return null or the current reference sequence
*/
SequenceI getSeqrep();
+
/**
- * set the reference or representative sequence for this collection.
- * Reference is assumed to be present within the collection.
+ * set the reference or representative sequence for this collection. Reference
+ * is assumed to be present within the collection.
+ *
* @return
*/
void setSeqrep(SequenceI refseq);
}
private boolean dummy = true;
+
/**
* become a proxy for mseq, merging any existing annotation on this sequence
*
public void become(SequenceI mseq)
{
initSeqFrom(mseq, null);
- dummy=false;
+ dummy = false;
}
/**
*/
package jalview.datamodel;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
/**
* Collects a set contiguous ranges on a set of sequences
*
{
synchronized (sequences)
{
- if (sequences.contains(s))
- {
- deleteSequence(s, recalc);
- }
- else
- {
- addSequence(s, recalc);
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ else
+ {
+ addSequence(s, recalc);
}
}
}
synchronized (sequences)
{
// MC This needs to get reset when characters are inserted and deleted
- boolean first=true;
- for (SequenceI seq:sequences) {
+ boolean first = true;
+ for (SequenceI seq : sequences)
+ {
if (first || seq.getLength() > width)
{
width = seq.getLength();
/**
* DOCUMENT ME!
+ *
* @param position
* DOCUMENT ME!
* @param ch
/**
* Transfer any database references or annotation from entry under a sequence
* mapping. <br/>
- * <strong>Note: DOES NOT transfer sequence associated alignment
- * annotation </strong><br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
*
* @param entry
* @param mp
*/
package jalview.datamodel;
-import java.awt.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
private String pdbId;
private List<SequenceI> seqList;
+
// TODO and possibly a list of chains?
/**
dna.addDBRef(retrievedref);
// add map to indicate the sequence is a valid coordinate frame for the
// dbref
- retrievedref.setMap(new Mapping(null, new int[]
- { 1, dna.getLength() }, new int[]
- { 1, dna.getLength() }, 1, 1));
+ retrievedref.setMap(new Mapping(null,
+ new int[] { 1, dna.getLength() }, new int[] { 1,
+ dna.getLength() }, 1, 1));
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
{
}
try
{
- for (EmblFeature feature: features)
+ for (EmblFeature feature : features)
{
if (!noNa)
{
.println("Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are
// marked.
- exon = new int[]
- { dna.getStart() + (prstart - 1), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { 1, prseq.length() }, 3, 1);
+ exon = new int[] { dna.getStart() + (prstart - 1), dna.getEnd() };
+ map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+ prseq.length() }, 3, 1);
}
if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
{
System.err
.println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exon = new int[]
- { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { 1, prseq.length() }, 3, 1);
+ exon = new int[] { dna.getStart() + (prstart - 1),
+ dna.getEnd() - 3 };
+ map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+ prseq.length() }, 3, 1);
}
}
else
// final product length trunctation check
map = new jalview.datamodel.Mapping(product,
- adjustForProteinLength(prseq.length(), exon), new int[]
- { 1, prseq.length() }, 3, 1);
+ adjustForProteinLength(prseq.length(), exon), new int[] {
+ 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
// TODO: this is only necessary when there codon annotation is
// complete (I think JBPNote)
pcdnaref.setAccessionId(prid);
pcdnaref.setSource(DBRefSource.EMBLCDS);
pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
- jalview.util.MapList mp = new jalview.util.MapList(new int[]
- { 1, prseq.length() }, new int[]
- { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
+ jalview.util.MapList mp = new jalview.util.MapList(new int[] { 1,
+ prseq.length() }, new int[] { 1 + (prstart - 1),
+ (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
// 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
// { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
*/
package jalview.datamodel.xdb.embl;
-import java.util.Vector;
-
import jalview.datamodel.DBRefEntry;
+import java.util.Vector;
+
/**
* Data model for a <feature> element returned from an EMBL query reply
*
try
{
// uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache.getDefault(
- jalview.bin.Cache.CASTORLOGLEVEL, "debug")
- .equalsIgnoreCase("DEBUG"))
+ if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
+ "debug").equalsIgnoreCase("DEBUG"))
{
unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
}
public void superposeStructures(AlignmentI alignment, int refStructure,
ColumnSelection hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
}
/**
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
- System.out
-.println("Superimpose command(s):\n" + cmdString);
+ System.out.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
for (String cbyseq : cpdbbyseq.commands)
{
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- return JmolCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr,
- alignment);
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
/**
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
- int colour = viewer.ms.at[atomIndex]
- .atomPropertyInt(T.color);
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
return new Color(colour);
}
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
- pdbfilename = new File(
- viewer.ms.getModelFileName(mnumber))
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
}
- // search pdbentries and sequences to find correct pdbentry for this
- // model
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
showConsole(false);
}
}
-
null, "-x -o -n", this);
} catch (ClassCastException x)
{
- throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
- x);
+ throw new Error(MessageManager.formatMessage(
+ "error.jmol_version_not_compatible_with_jalview_version",
+ new String[] { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
* equivalent (e.g. MSE with MET->M) to maximise sequence matching
*/
String threeLetterCode = group.getGroup3();
- String canonical = ResidueProperties.getCanonicalAminoAcid(threeLetterCode);
+ String canonical = ResidueProperties
+ .getCanonicalAminoAcid(threeLetterCode);
if (canonical != null
&& !canonical.equalsIgnoreCase(threeLetterCode))
{
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
- final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+ final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
+ twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
return readers.iterator();
@Override
public void remove()
{
- throw new Error(MessageManager.getString("error.not_implemented_remove"));
+ throw new Error(
+ MessageManager.getString("error.not_implemented_remove"));
}
@Override
protected Object clone() throws CloneNotSupportedException
{
- throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
+ throw new CloneNotSupportedException(
+ MessageManager.getString("error.not_implemented_clone"));
}
@Override
};
} catch (Exception foo)
{
- throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
+ throw new Exception(
+ MessageManager
+ .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+ foo);
}
}
*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
ChimeraCommands.class, null,
colourCommands.toArray(new String[0]));
- return new StructureMappingcommandSet[]
- { cs };
+ return new StructureMappingcommandSet[] { cs };
}
/**
* <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
* #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
*
- * @see http
+ * @see http
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
* .html </pre>
*
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
boolean firstModelForColour = true;
- final Map<Integer, Map<String, List<int[]>>> colourData = colourMap.get(colour);
+ final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+ .get(colour);
for (Integer model : colourData.keySet())
{
boolean firstPositionForModel = true;
/*
* Add the start/end positions
*/
- chainData.add(new int[]
- { startPos, endPos });
+ chainData.add(new int[] { startPos, endPos });
}
}
package jalview.ext.rbvi.chimera;
+import jalview.httpserver.AbstractRequestHandler;
+import jalview.structure.SelectionSource;
+
import java.net.BindException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import jalview.httpserver.AbstractRequestHandler;
-import jalview.structure.SelectionSource;
-
/**
* This is a simple Http handler that can listen for selections in Chimera.
* <p/>
{
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[]
- { this });
+ JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop,
MessageManager.getString("label.export_settings"));
dialog.addWindowListener(new WindowAdapter()
}
}
-
public void ok_actionPerformed(ActionEvent e)
{
cancelled = false;
this(al, hiddenColumns, width, height, null);
}
-
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
alignPanel = new AlignmentPanel(this, viewport);
-
addAlignmentPanel(alignPanel, true);
init();
}
init();
}
-
/**
* Make a new AlignFrame from existing alignmentPanels
*
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
-
+
if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().insertGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().deleteGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode", new String[]
- { (viewport.cursorMode ? "on" : "off") }));
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
success = new Jalview2XML().saveAlignment(this, file, shortName);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
+ "label.successfully_saved_to_file_in_format", new Object[] {
+ fileName, format }));
}
else
}
FormatAdapter f = new FormatAdapter(alignPanel,
exportData.getSettings());
- String output = f.formatSequences(format,
+ String output = f.formatSequences(
+ format,
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[]
- { fileName, format }));
+ new Object[] { fileName, format }));
} catch (Exception ex)
{
success = false;
if (!success)
{
JOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }), MessageManager
+ .formatMessage("label.couldnt_save_file",
+ new Object[] { fileName }), MessageManager
.getString("label.error_saving_file"),
JOptionPane.WARNING_MESSAGE);
}
return success;
}
-
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
try
{
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(
- e.getActionCommand(),
- exportData.getAlignment(),
- exportData.getOmitHidden(), exportData.getStartEndPostions(),
- viewport.getColumnSelection()));
+ .formatSequences(e.getActionCommand(),
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getColumnSelection()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
}
- public static AlignmentExportData getAlignmentForExport(String exportFormat,
- AlignViewportI viewport,
+ public static AlignmentExportData getAlignmentForExport(
+ String exportFormat, AlignViewportI viewport,
AlignExportSettingI exportSettings)
{
AlignmentI alignmentToExport = null;
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
-
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = new int[]
- { 0, alignmentToExport.getWidth() - 1 };
+ alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
if (settings == null)
{
settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), exportFormat);
+ viewport.hasHiddenColumns(), exportFormat);
}
// settings.isExportAnnotations();
alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
.getColumnSelection().getHiddenColumns());
}
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
- settings);
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+ omitHidden, alignmentStartEnd, settings);
return ed;
}
}
// System.out.println("Export range : " + minPos + " - " + maxPos);
- return new int[]
- { startPos, endPos };
+ return new int[] { startPos, endPos };
}
public static void main(String[] args)
{
ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
- hiddenCols.add(new int[]
- { 0, 4 });
- hiddenCols.add(new int[]
- { 6, 9 });
- hiddenCols.add(new int[]
- { 11, 12 });
- hiddenCols.add(new int[]
- { 33, 33 });
- hiddenCols.add(new int[]
- { 45, 50 });
-
- int[] x = getStartEnd(new int[]
- { 0, 50 }, hiddenCols);
+ hiddenCols.add(new int[] { 0, 4 });
+ hiddenCols.add(new int[] { 6, 9 });
+ hiddenCols.add(new int[] { 11, 12 });
+ hiddenCols.add(new int[] { 33, 33 });
+ hiddenCols.add(new int[] { 45, 50 });
+
+ int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
// System.out.println("Export range : " + x[0] + " - " + x[1]);
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
+
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
{
alignPanel.makeSVG(f);
}
+
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setText(MessageManager.formatMessage(
- "label.undo_command", new Object[]
- { command.getDescription() }));
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
}
else
{
CommandI command = viewport.getRedoList().peek();
redoMenuItem.setText(MessageManager.formatMessage(
- "label.redo_command", new Object[]
- { command.getDescription() }));
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
}
else
{
}
if (viewport != null)
{
- return new AlignmentI[]
- { viewport.getAlignment() };
+ return new AlignmentI[] { viewport.getAlignment() };
}
return null;
}
boolean appendHistoryItem = false;
Deque<CommandI> historyList = viewport.getHistoryList();
boolean inSplitFrame = getSplitViewContainer() != null;
- if (!inSplitFrame && historyList != null
- && historyList.size() > 0
+ if (!inSplitFrame && historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
- hiddenColumns.add(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ hiddenColumns.add(new int[] { region[0] - hiddenOffset,
+ region[1] - hiddenOffset });
}
}
}
- Desktop.jalviewClipboard = new Object[]
- { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+ Desktop.jalviewClipboard = new Object[] { seqs,
+ viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText(MessageManager.formatMessage(
- "label.copied_sequences_to_clipboard", new Object[]
- { Integer.valueOf(seqs.length).toString() }));
+ "label.copied_sequences_to_clipboard", new Object[] { Integer
+ .valueOf(seqs.length).toString() }));
}
/**
//
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"),
- Action.PASTE,
- sequences, 0, alignment.getWidth(), alignment));
+ Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
}
statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns", new String[]
- { Integer.valueOf(trimRegion.getSize()).toString() }));
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns", new Object[]
- { Integer.valueOf(removeGapCols.getSize()).toString() }));
+ "label.removed_empty_columns",
+ new Object[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
// This is to maintain viewport position on first residue
// of first sequence
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
- .calculateIdWidth());
+ alignPanel.getIdPanel().getIdCanvas()
+ .setPreferredSize(alignPanel.calculateIdWidth());
alignPanel.paintAlignment(true);
}
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
-// alignPanel.paintAlignment(true);
+ // alignPanel.paintAlignment(true);
}
/**
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
editPane.setText(MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() }));
+ new Object[] { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new Object[]
- { getTitle() }), 500, 400);
+ "label.alignment_properties", new Object[] { getTitle() }),
+ 500, 400);
}
/**
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new Object[]
- { this.getTitle() }), frame.getWidth(), frame.getHeight());
+ "label.overview_params", new Object[] { this.getTitle() }),
+ frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
+ "action.by_title_param", new Object[] { title }));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
calculateTree.removeAll();
// build the calculate menu
- for (final String type : new String[]
- { "NJ", "AV" })
+ for (final String type : new String[] { "NJ", "AV" })
{
String treecalcnm = MessageManager.getString("label.tree_calc_"
+ type.toLowerCase());
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
if (!viewport.getAlignment().isAligned(false))
{
- seqs.setSequences(new SeqCigar[]
- { seqs.getSequences()[0] });
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
// TODO: if seqs.getSequences().length>1 then should really have warned
// user!
{
final long sttime = System.currentTimeMillis();
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from", new Object[]
- { source }), sttime);
+ "status.searching_for_sequences_from",
+ new Object[] { source }), sttime);
try
{
// update our local dataset reference
}
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
"status.finished_searching_for_sequences_from",
- new Object[]
- { source }),
- sttime);
+ new Object[] { source }), sttime);
}
};
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager.formatMessage(
- "label.translation_of_params", new Object[]
- { this.getTitle() });
+ "label.translation_of_params",
+ new Object[] { this.getTitle() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
{
return avc.parseFeaturesFile(file, type,
jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-
+
}
@Override
showSeqFeatures.setSelected(true);
}
-
}
+
@Override
public void dragEnter(DropTargetDragEvent evt)
{
{
if (type.equalsIgnoreCase("PDB"))
{
- filesmatched.add(new Object[]
- { file, protocol, mtch });
+ filesmatched.add(new Object[] { file, protocol, mtch });
continue;
}
}
MessageManager
.formatMessage(
"label.automatically_associate_pdb_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(
- filesmatched
- .size())
+ new Object[] { Integer
+ .valueOf(
+ filesmatched
+ .size())
.toString() }),
MessageManager
.getString("label.automatically_associate_pdb_files_by_name"),
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- "<html>"+MessageManager
- .formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[]
- { Integer.valueOf(
- filesnotmatched
- .size())
- .toString() })+"</html>",
+ "<html>"
+ + MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[] { Integer
+ .valueOf(
+ filesnotmatched
+ .size())
+ .toString() })
+ + "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .annotateAlignmentView(viewport, file, protocol)
- : false;
+ .annotateAlignmentView(viewport, file, protocol) : false;
if (!isAnnotation)
{
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage(
+ "label.fetch_retrieve_from",
+ new Object[] { src.getDbName() })));
dfetch.add(fetchr);
comp++;
}
// fetch all entry
DbSourceProxy src = otherdb.get(0);
fetchr = new JMenuItem(MessageManager.formatMessage(
- "label.fetch_all_param", new Object[]
- { src.getDbSource() }));
+ "label.fetch_all_param",
+ new Object[] { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage(
+ "label.fetch_retrieve_from_all_sources",
+ new Object[] {
+ Integer.valueOf(otherdb.size())
+ .toString(), src.getDbSource(),
+ src.getDbName() })));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
- ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
+ ifetch = new JMenu(MessageManager.formatMessage(
+ "label.source_from_db_source",
+ new Object[] { src.getDbSource() }));
icomp = 0;
String imname = null;
int i = 0;
0, 10) + "..." : dbname;
if (imname == null)
{
- imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
+ imname = MessageManager.formatMessage(
+ "label.from_msname", new Object[] { sname });
}
fetchr = new JMenuItem(msname);
- final DbSourceProxy[] dassrc =
- { sproxy };
+ final DbSourceProxy[] dassrc = { sproxy };
fetchr.addActionListener(new ActionListener()
{
});
fetchr.setToolTipText("<html>"
- + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
+ + MessageManager.formatMessage(
+ "label.fetch_retrieve_from", new Object[]
+ { dbname }));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
alignPanel.paintAlignment(true);
}
}
+
public void clearAlignmentSeqRep()
{
// TODO refactor alignmentseqrep to controller
- if (viewport.getAlignment().hasSeqrep()) {
+ if (viewport.getAlignment().hasSeqrep())
+ {
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
if (!viewport.getSequenceSetId().equals(
alignmentPanel.av.getSequenceSetId()))
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null
&& tabbedPane.getTabCount() > 0
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel)
- : alignPanels;
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
}
/**
return;
}
List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
- for (SequenceI aaSeq : alignment.getSequences()) {
- for (AlignedCodonFrame acf : mappings) {
+ for (SequenceI aaSeq : alignment.getSequences())
+ {
+ for (AlignedCodonFrame acf : mappings)
+ {
SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
if (dnaSeq != null)
{
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ this.title;
Desktop.addInternalFrame(alignFrame, newtitle,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
/**
protected void showComplement_actionPerformed(boolean show)
{
SplitContainerI sf = getSplitViewContainer();
- if (sf != null) {
+ if (sf != null)
+ {
sf.setComplementVisible(this, show);
}
}
private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
+
/**
* Creates a new AlignViewport object.
*
viewStyle.getFontSize()), false);
}
+
/**
* DOCUMENT ME!
*
// TODO: JAL-1126
if (historyList == null || redoList == null)
{
- return new long[]
- { -1, -1 };
+ return new long[] { -1, -1 };
}
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
}
/**
List<SequenceI> seqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq
- .getDatasetSequence().getAllPDBEntries();
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
if (pdbs == null)
{
continue;
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[]
- { MessageManager.getString("action.no"),
+ String[] options = new String[] {
+ MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[]
- { title }));
+ "label.successfully_loaded_file", new Object[] { title }));
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
if (openInNewWindow)
{
Desktop.addInternalFrame(newAlignFrame, title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
try
{
newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN",
- false));
+ "SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
- * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
*/
AlignFrame copyMe = new AlignFrame(complement,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
: newAlignFrame;
- final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
- : copyMe;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
cdnaFrame.setVisible(true);
proteinFrame.setVisible(true);
String linkedTitle = MessageManager
if (!sr.isEmpty())
{
// TODO would like next line without cast but needs more refactoring...
- final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
complementPanel.setFollowingComplementScroll(true);
complementPanel.scrollToCentre(sr, verticalOffset);
}
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
{
return av;
}
+
public void alignmentChanged()
{
av.alignmentChanged(this);
scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight()
- + fm.getDescent()));
+ .getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+ public boolean scrollToPosition(SearchResults searchResults,
+ boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
}
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
- int verticalOffset,
- boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
// TODO: properly locate search results in view when large numbers of hidden
int start = r[0];
int end = r[1];
// DEBUG
-// System.err.println(this.av.viewName + " Seq : " + seqIndex
-// + " Scroll to " + start + "," + end);
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment()
- .getAlignmentAnnotation(),
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
repaint();
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw main sequence panel
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+ endSeq, 0);
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
}
if (labels != null)
{
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
+ pg.translate(
+ +3,
+ -ypos
- (av.getAlignment().getHeight() * av
.getCharHeight()));
}
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[]
- { type.getLabel() }), progress);
+ "status.saving_file", new Object[] { type.getLabel() }),
+ progress);
}
try
{
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+ alignFrame.setProgressBar(
+ MessageManager.getString("status.export_complete"),
+ progress);
}
}
}
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
+
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res)
- + "");
+ .getCharAt(res) + "");
}
else
{
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
return av == null ? null : av.getAlignment();
}
-
@Override
public String getViewName()
{
return new FeatureRenderer(this);
}
- @Override
+
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
- public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
// currently selected 'annotation type' checkboxes
private Map<String, String> selectedTypes = new HashMap<String, String>();
-
+
/**
* Constructor.
*
final boolean wholeAlignment = this.sg == null;
JPanel applyToOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
CheckboxGroup actingOn = new CheckboxGroup();
-
+
String forAll = MessageManager.getString("label.all_sequences");
final Checkbox allSequences = new Checkbox(forAll, actingOn,
wholeAlignment);
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getStateChange() == ItemEvent.SELECTED) {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
AnnotationChooser.this.setApplyToSelectedSequences(true);
AnnotationChooser.this.setApplyToUnselectedSequences(true);
AnnotationChooser.this.changeApplyTo_actionPerformed();
}
});
applyToOptions.add(allSequences);
-
+
String forSelected = MessageManager
.getString("label.selected_sequences");
final Checkbox selectedSequences = new Checkbox(forSelected, actingOn,
}
});
applyToOptions.add(selectedSequences);
-
+
String exceptSelected = MessageManager
.getString("label.except_selected_sequences");
- final Checkbox unselectedSequences = new Checkbox(exceptSelected, actingOn, false);
+ final Checkbox unselectedSequences = new Checkbox(exceptSelected,
+ actingOn, false);
unselectedSequences.setEnabled(!wholeAlignment);
unselectedSequences.addItemListener(new ItemListener()
{
}
});
applyToOptions.add(unselectedSequences);
-
+
// set member variables to match the initial selection state
this.applyToSelectedSequences = selectedSequences.getState()
|| allSequences.getState();
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getStateChange() == ItemEvent.SELECTED) {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
AnnotationChooser.this.setShowSelected(true);
AnnotationChooser.this.changeShowHide_actionPerformed();
}
{
JPanel jp = new JPanel();
final Font labelFont = JvSwingUtils.getLabelFont();
-
+
JButton ok = new JButton(MessageManager.getString("action.ok"));
ok.setFont(labelFont);
ok.addActionListener(new ActionListener()
}
});
jp.add(ok);
-
+
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(labelFont);
cancel.addActionListener(new ActionListener()
JButton defColours = new JButton();
-
JPanel jPanel1 = new JPanel();
JPanel jPanel2 = new JPanel();
getThreshold().setSelectedIndex(2);
break;
default:
- throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_dont_know_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
&& getCurrentAnnotation().threshold == null)
{
getCurrentAnnotation()
- .setThreshold(new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
.getLayout());
+
private JPanel noGraphFilterView = new JPanel();
private JPanel graphFilterView = new JPanel();
slider.setToolTipText(defaultTtip);
}
}
+
public void reset()
{
if (this.getOldColumnSelection() != null)
updateView();
}
-
public class FurtherActionPanel extends JPanel
{
private AnnotationColumnChooser aColChooser;
{
if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
{
- this.optionsGroup.setSelected(this.hideOption.getModel(),
- true);
+ this.optionsGroup.setSelected(this.hideOption.getModel(), true);
}
else
{
JvSwingUtils.jvInitComponent(searchBox);
searchBox.setToolTipText(MessageManager
.getString("info.enter_search_text_here"));
- searchBox.getDocument().addDocumentListener(
- new DocumentListener()
- {
- @Override
- public void insertUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
- });
+ searchBox.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+ });
JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.setEnabled(false);
{
String defaultTtip = MessageManager
.getString("info.enter_search_text_to_enable");
- String labelTtip = MessageManager
-.formatMessage(
+ String labelTtip = MessageManager.formatMessage(
"info.search_in_annotation_label", annotations
.getSelectedItem().toString());
- String descTtip = MessageManager
-.formatMessage(
+ String descTtip = MessageManager.formatMessage(
"info.search_in_annotation_description", annotations
.getSelectedItem().toString());
- displayName.setToolTipText(displayName.isEnabled() ? labelTtip : defaultTtip);
+ displayName.setToolTipText(displayName.isEnabled() ? labelTtip
+ : defaultTtip);
description.setToolTipText(description.isEnabled() ? descTtip
: defaultTtip);
}
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
- : MessageManager.getString("label.save_annotation_to_file"));
+ chooser.setDialogTitle(features ? MessageManager
+ .getString("label.save_features_to_file") : MessageManager
+ .getString("label.save_annotation_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
return text;
}
+
public void toTextbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
Desktop.addInternalFrame(
cap,
(features ? MessageManager.formatMessage(
- "label.features_for_params", new String[]
- { ap.alignFrame.getTitle() }) : MessageManager
- .formatMessage("label.annotations_for_params",
- new String[]
- { ap.alignFrame.getTitle() })), 600, 500);
+ "label.features_for_params",
+ new String[] { ap.alignFrame.getTitle() })
+ : MessageManager.formatMessage(
+ "label.annotations_for_params",
+ new String[] { ap.alignFrame.getTitle() })),
+ 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning((features ? MessageManager.formatMessage(
- "label.generating_features_for_params", new String[]
- { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
- "label.generating_annotations_for_params", new String[]
- { ap.alignFrame.getTitle() })), oom);
+ "label.generating_features_for_params",
+ new String[] { ap.alignFrame.getTitle() })
+ : MessageManager.formatMessage(
+ "label.generating_annotations_for_params",
+ new String[] { ap.alignFrame.getTitle() })), oom);
cap.dispose();
}
close_actionPerformed(null);
}
+
public void close_actionPerformed(ActionEvent e)
{
try
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
- String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+ String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
String ADDNEW = MessageManager.getString("label.add_new_row");
- String EDITNAME = MessageManager.getString("label.edit_label_description");
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
String HIDE = MessageManager.getString("label.hide_row");
String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
- String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+ String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
boolean resizePanel = false;
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- new AlignmentAnnotation[]
- { aa[selectedRow] });
+ new AlignmentAnnotation[] { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
}
else
{
- ap.getSeqPanel().ap.getIdPanel()
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
}
return;
}
{
if (evt.getClickCount() == 1)
{
- ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
+ ap.getSeqPanel().ap
+ .getIdPanel()
+ .highlightSearchResults(
+ Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- // we make a copy rather than edit the current selection if no modifiers pressed
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
- } else {
+ }
+ else
+ {
if (evt.isControlDown())
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
- } else {
- // notionally, we should also add intermediate sequences from last added sequence ?
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
sg.addSequence(aa[selectedRow].sequenceRef, true);
}
}
- } else {
+ }
+ else
+ {
sg = new SequenceGroup();
sg.setStartRes(0);
- sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
{
final String label = aa[selectedRow].label;
JMenuItem hideType = new JMenuItem();
- String text = MessageManager.getString("label.hide_all") + " " + label;
+ String text = MessageManager.getString("label.hide_all") + " "
+ + label;
hideType.setText(text);
hideType.addActionListener(new ActionListener()
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
.isIgnoreGapsConsensus());
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics());
+ ap.getAnnotationPanel().paint(
+ ap.getAnnotationPanel().getGraphics());
}
else
{
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
- SequenceI[] seqs = new SequenceI[]
- { sq };
+ SequenceI[] seqs = new SequenceI[] { sq };
String[] omitHidden = null;
- SequenceI[] dseqs = new SequenceI[]
- { sq.getDatasetSequence() };
+ SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
if (dseqs[0] == null)
{
dseqs[0] = new Sequence(sq);
sq.getLength(), seqs);
}
- int[] alignmentStartEnd = new int[]
- { 0, ds.getWidth() - 1 };
+ int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
if (hiddenCols != null)
{
hiddenColumns = new ArrayList<int[]>();
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- hiddenColumns.add(new int[]
- { region[0], region[1] });
+ hiddenColumns.add(new int[] { region[0], region[1] });
}
}
- Desktop.jalviewClipboard = new Object[]
- { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+ Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+ // of a consensus
+ // sequence ? need to
+ // flag
// sequence as special.
hiddenColumns };
}
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
- .getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+ .getAnnotationPanel().getVisibleVRange() : null;
if (clip && visr != null)
{
sOffset = visr[0];
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_foreground_colour"), Color.black);
+ MessageManager.getString("label.select_foreground_colour"),
+ Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
anot[index] = new Annotation(label, "", type, 0);
}
-
anot[index].secondaryStructure = type != 'S' ? type : label
.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText(JvSwingUtils
- .wrapTooltip(true, aa[row].annotations[res].description));
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aa[row].annotations[res].description));
}
else
{
{
try
{
- image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
+ .getHeight(), BufferedImage.TYPE_INT_RGB);
} catch (OutOfMemoryError oom)
{
try
});
}
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
return false;
}
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[]
- { new Integer(_alignwith.size()).toString() }));
+ new String[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
}
try
{
}
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
try
{
// TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
- "Make PNG image from view", width, height, null, null);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle());
}
else
{
@Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"), null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
@Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
SecondaryStructureListener, InterfaceVARNASelectionListener,
VamsasSource
{
- private static final byte[] PAIRS = new byte[]
- { '(', ')', '[', ']', '{', '}', '<', '>' };
+ private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+ '}', '<', '>' };
private AppVarnaBinding vab;
String theTitle = sname
+ (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
theTitle = MessageManager.formatMessage("label.varna_params",
- new String[]
- { theTitle });
+ new String[] { theTitle });
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
vab.setSelectedIndex(0);
}
-
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
vab.setSelectedIndex(selectedIndex);
}
-
/**
* Add a model with associated Varna session file
*
}
}
-
/**
* Replace everything except RNA secondary structure characters with a period
*
_sideList.addMouseListener(new MouseAdapter()
{
@Override
- public void mouseClicked(MouseEvent e) {
+ public void mouseClicked(MouseEvent e)
+ {
AppVarnaBinding.this.mouseClicked(e);
}
});
_listPanel.add(j, BorderLayout.NORTH);
_listPanel.add(listScroller, BorderLayout.CENTER);
- new DropTarget(vp, new DropTargetAdapter() {
+ new DropTarget(vp, new DropTargetAdapter()
+ {
@Override
public void drop(DropTargetDropEvent dtde)
{
public String[][] getParameterInfo()
{
- String[][] info =
- {
+ String[][] info = {
// Parameter Name Kind of Value Description,
{ "sequenceDBN", "String", "A raw RNA sequence" },
{ "structureDBN", "String",
{
name += " (Model " + mn++ + ")";
}
- _rnaList.add(varnaPanel.getConfig().clone(), r, name, true);
+ _rnaList.add(varnaPanel.getConfig().clone(), r, name,
+ true);
}
}
}
* restore the previous display
*/
vp.showRNA(sel.rna, sel.config);
-
+
return filePath;
} catch (IOException e)
{
*
* @param evt
*/
- protected void changeSelectedStructure_actionPerformed(ListSelectionEvent evt)
+ protected void changeSelectedStructure_actionPerformed(
+ ListSelectionEvent evt)
{
if (!evt.getValueIsAdjusting())
{
PDBEntry entry = new PDBEntry();
MCview.PDBfile pdbfile = null;
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[]
- { sequence }, null, choice, protocol);
+ .setMapping(false, new SequenceI[] { sequence }, null, choice,
+ protocol);
if (pdbfile == null)
{
// stacktrace already thrown so just return
{
createDialog();
bounds = new Rectangle(5, 5, 550, 350);
- jd.initDialogFrame(me, false, false, MessageManager.getString("label.news_from_jalview"),
+ jd.initDialogFrame(me, false, false,
+ MessageManager.getString("label.news_from_jalview"),
bounds.width, bounds.height);
jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
Cache.log.debug("Displaying news.");
topBottomSplitPane.setBottomComponent(bottomPanel);
JScrollPane spTextDescription = new JScrollPane(textDescription);
textDescription.setText("");
- statusBar.setText(new StringBuffer("[").append(MessageManager.getString("label.status")).append("]").toString());
+ statusBar.setText(new StringBuffer("[")
+ .append(MessageManager.getString("label.status")).append("]")
+ .toString());
buttonRefresh.addActionListener(new ActionListener()
{
component
.setText(MessageManager.formatMessage(
"label.channel_title_item_count",
- new String[]
- {
+ new String[] {
channel.getTitle(),
Integer.valueOf(channel.getUnreadItemCount())
.toString() }));
{
component.setText(MessageManager.formatMessage(
"label.blog_item_published_on_date",
- new String[]
- {
+ new String[] {
DateFormat
.getDateInstance(DateFormat.LONG,
MessageManager.getLocale())
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
String chain = null;
if (seq.getDatasetSequence() != null)
{
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
+ Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
+ .getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
chain = pdbrefs.get(0).getChainCode();
* @param newViewId
*/
public ChimeraViewFrame(String chimeraSessionFile,
- AlignmentPanel alignPanel,
- PDBEntry[] pdbArray,
+ AlignmentPanel alignPanel, PDBEntry[] pdbArray,
SequenceI[][] seqsArray, boolean colourByChimera,
boolean colourBySequence, String newViewId)
{
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
if (!jmb.launchChimera())
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
+ JOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
JOptionPane.ERROR_MESSAGE);
if (!closeChimera)
{
String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", false) });
+ "label.confirm_close_chimera",
+ new Object[] { jmb.getViewerTitle("Chimera", false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
}
// Explicitly map to the filename used by Chimera ;
jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos],
- pe.getFile(),
- protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
+ new Object[] { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- msg = pdbid + " "
- + MessageManager.getString("label.state_completed");
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// stopProgressBar(msg, hdl);
}
import jalview.util.MessageManager;
-import java.io.*;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GraphicsEnvironment;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.IOException;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import org.apache.log4j.SimpleLayout;
} catch (InterruptedException ie)
{
}
- throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
+ throw new NullPointerException(
+ MessageManager.getString("exception.application_test_npe"));
}
}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteHtmlTransfer;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
import java.io.StringWriter;
-import javax.swing.*;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
import javax.swing.event.HyperlinkEvent.EventType;
-
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
+import javax.swing.event.HyperlinkListener;
/**
* Cut'n'paste files into the desktop See JAL-1105
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
AlignViewportI viewport;
FileParse source = null;
+
public CutAndPasteTransfer()
{
SwingUtilities.invokeLater(new Runnable()
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.couldnt_read_pasted_text", new String[]
- { ex.toString() }), MessageManager
+ "label.couldnt_read_pasted_text",
+ new String[] { ex.toString() }), MessageManager
.getString("label.error_parsing_text"),
JOptionPane.WARNING_MESSAGE);
}
if (al != null && al.hasValidSequence())
{
String title = MessageManager.formatMessage(
- "label.input_cut_paste_params", new String[]
- { format });
+ "label.input_cut_paste_params", new String[] { format });
if (viewport != null)
{
((AlignViewport) viewport).addAlignment(al, title);
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
af.changeColour(cs);
}
}
-
/**
* DOCUMENT ME!
*
*/
package jalview.gui;
+import jalview.jbgui.GDasSourceBrowser;
+import jalview.util.MessageManager;
+import jalview.util.TableSorter;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import org.biodas.jdas.schema.sources.PROP;
import org.biodas.jdas.schema.sources.VERSION;
-import jalview.jbgui.GDasSourceBrowser;
-import jalview.util.MessageManager;
-import jalview.util.TableSorter;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
public class DasSourceBrowser extends GDasSourceBrowser implements
Runnable, ListSelectionListener
{
return;
}
- Object[] options =
- { "Edit", "Remove", "Cancel" };
+ Object[] options = { "Edit", "Remove", "Cancel" };
int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
"Do you want to edit or remove " + nickname + "?",
"Edit / Remove Local DAS Source",
// The features filter is not visible, but we must still
// filter the das source list here.
// July 2006 - only 6 sources fo not serve features
- Object[] dummyFeatureList = new Object[]
- { "features" };
+ Object[] dummyFeatureList = new Object[] { "features" };
List<jalviewSourceI> srcs = sourceRegistry.getSources();
for (jalviewSourceI ds : srcs)
{
for (int j = 0; j < coords.size(); j++)
{
- if (selectedInList(filter1.getSelectedValues(), new String[]
- { coords.get(j).getAuthority() })
+ if (selectedInList(filter1.getSelectedValues(),
+ new String[] { coords.get(j).getAuthority() })
&& selectedInList(filter2.getSelectedValues(), new String[]
{ coords.get(j).getSource() }))
{
this.data = data;
}
- private String[] columnNames = new String[]
- { MessageManager.getString("label.nickname"), MessageManager.getString("label.use_source") };
+ private String[] columnNames = new String[] {
+ MessageManager.getString("label.nickname"),
+ MessageManager.getString("label.use_source") };
private Object[][] data;
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
- { url }), MessageManager
+ new Object[] { url }), MessageManager
.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
public void saveState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "jvp" }, new String[] { "Jalview Project" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
{
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
- "label.saving_jalview_project", new Object[]
- { choice.getName() }), choice.hashCode());
+ "label.saving_jalview_project",
+ new Object[] { choice.getName() }), choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
// TODO catch and handle errors for savestate
ex);
JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
- new Object[]
- { choice.getName() }), MessageManager
+ new Object[] { choice.getName() }), MessageManager
.getString("label.couldnt_save_project"),
JOptionPane.WARNING_MESSAGE);
}
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" }, new String[]
- { "Jalview Project", "Jalview Project (old)" },
- "Jalview Project");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+ "jvp", "jar" }, new String[] { "Jalview Project",
+ "Jalview Project (old)" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
{
public void run()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
+ setProgressBar(
+ MessageManager.formatMessage(
+ "label.loading_jalview_project",
+ new Object[] { choice }), choice.hashCode());
try
{
new Jalview2XML().loadJalviewAlign(choice);
JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.error_whilst_loading_project_from",
- new Object[]
- { choice }), MessageManager
+ new Object[] { choice }), MessageManager
.getString("label.couldnt_load_project"),
JOptionPane.WARNING_MESSAGE);
}
if (fileLoadingCount == 0)
{
fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
- "label.loading_file", new Object[]
- { fileName })));
+ "label.loading_file", new Object[] { fileName })));
}
fileLoadingCount++;
}
{
for (AlignmentPanel ap : af.alignPanels)
{
- if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId()))
+ if (alignmentId == null
+ || alignmentId.equals(ap.av.getSequenceSetId()))
{
aps.add(ap);
}
for (AlignFrame afr : frames)
{
- if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+ if (sequenceSetId == null
+ || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
if (afr.alignPanels != null)
{
Desktop.desktop,
MessageManager.formatMessage(
"label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
+ new Object[] { fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
return v_client.inSession();
}
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
sessit.setToolTipText(MessageManager.formatMessage(
- "label.connect_to_session", new Object[]
- { sess[i] }));
+ "label.connect_to_session", new Object[] { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- new String[]
- { "Vamsas Document" }, "Vamsas Document");
+ new String[] { "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
{
java.io.File choice = chooser.getSelectedFile();
JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
- "label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
+ "label.saving_vamsas_doc",
+ new Object[] { choice.getName() }));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
{
g.drawString(MessageManager.formatMessage(
"label.memory_stats",
- new Object[]
- { df.format(totalFreeMemory), df.format(maxMemory),
- df.format(percentUsage) }), 10,
+ new Object[] { df.format(totalFreeMemory),
+ df.format(maxMemory), df.format(percentUsage) }), 10,
getHeight() - fm.getHeight());
}
}
"groovy.ui.Console");
Constructor<?> gccons = gcClass.getConstructor();
java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
- new Class[]
- { String.class, Object.class });
+ new Class[] { String.class, Object.class });
java.lang.reflect.Method run = gcClass.getMethod("run");
Object gc = gccons.newInstance();
- setvar.invoke(gc, new Object[]
- { "Jalview", this });
+ setvar.invoke(gc, new Object[] { "Jalview", this });
run.invoke(gc);
} catch (Exception ex)
{
{
handler.cancelActivity(id);
us.setProgressBar(MessageManager.formatMessage(
- "label.cancelled_params", new Object[]
- { ((JLabel) progressPanel.getComponent(0)).getText() }),
- id);
+ "label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0))
+ .getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
/**
- * This will return the first AlignFrame holding the given viewport instance. It
- * will break if there are more than one AlignFrames viewing a particular av.
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
* @param viewport
* @return alignFrame for viewport
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(viewport
- .getSequenceSetId());
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
for (int panel = 0; aps != null && panel < aps.length; panel++)
{
if (aps[panel] != null && aps[panel].av == viewport)
if (progress != null)
{
progress.setProgressBar(MessageManager.formatMessage(
- "status.opening_params", new Object[]
- { url }), this.hashCode());
+ "status.opening_params", new Object[] { url }), this
+ .hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
-
+
JInternalFrame[] frames = desktop.getAllFrames();
for (JInternalFrame frame : frames)
{
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
}
-
+
if (gatherThis)
{
topFrame.getAlignPanels().clear();
Desktop.currentAlignFrame = currentAlignFrame;
}
-
}
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
public class EPSOptions extends JPanel
{
bg.add(text);
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[]
- { this });
+ JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
dialog.setVisible(true);
import jalview.util.MessageManager;
-import java.awt.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
public class EditNameDialog
{
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.LineBorder;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+import javax.swing.BorderFactory;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
public class FeatureColourChooser extends JalviewDialog
{
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer implements
+ jalview.api.FeatureRenderer
{
Color resBoxColour;
super();
this.ap = ap;
this.av = ap.av;
- if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
+ if (ap != null && ap.getSeqPanel() != null
+ && ap.getSeqPanel().seqCanvas != null
&& ap.getSeqPanel().seqCanvas.fr != null)
{
transferSettings(ap.getSeqPanel().seqCanvas.fr);
if (fcol instanceof Color)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"),
+ ((Color) fcol));
if (col != null)
{
fcol = col;
Object[] options;
if (!newFeatures)
{
- options = new Object[]
- { "Amend", "Delete", "Cancel" };
+ options = new Object[] { "Amend", "Delete", "Cancel" };
}
else
{
- options = new Object[]
- { "OK", "Cancel" };
+ options = new Object[] { "OK", "Cancel" };
}
- String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
+ JOptionPane.QUESTION_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
return true;
}
-
/**
* update the amend feature button dependent on the given style
*
this.af = af;
fr = af.getFeatureRenderer();
// allow transparency to be recovered
- transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100));
+ transparency.setMaximum(100 - (int) ((originalTransparency = fr
+ .getTransparency()) * 100));
try
{
ex.printStackTrace();
}
- table = new JTable() {
+ table = new JTable()
+ {
@Override
- public String getToolTipText(MouseEvent e) {
- if (table.columnAtPoint(e.getPoint()) == 0) {
+ public String getToolTipText(MouseEvent e)
+ {
+ if (table.columnAtPoint(e.getPoint()) == 0)
+ {
/*
* Tooltip for feature name only
*/
- return JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.feature_settings_click_drag"));
+ return JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.feature_settings_click_drag"));
}
return null;
}
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(),
- evt.getY());
+ evt.getX(), evt.getY());
}
}
});
}
}
});
-// table.setToolTipText(JvSwingUtils.wrapTooltip(true,
-// MessageManager.getString("label.feature_settings_click_drag")));
+ // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ // MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
final Object typeCol, final Hashtable minmax, int x, int y)
{
JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
- "label.settings_for_param", new String[]
- { type }));
+ "label.settings_for_param", new String[] { type }));
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureScore(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
}
});
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
}
});
af.alignPanel.overviewPanel.updateOverviewImage();
}
- resetTable(new String[]
- { grp });
+ resetTable(new String[] { grp });
}
});
groupPanel.add(check);
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "fc" },
+ new String[] { "Sequence Feature Colours" },
+ "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
file), "UTF-8");
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = jucs
- .unmarshal(in);
+ jucs = jucs.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "fc" },
+ new String[] { "Sequence Feature Colours" },
+ "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
}
if (sort)
- {
+ {
jalview.util.QuickSort.sort(width, data);
- // update global priority order
+ // update global priority order
}
updateFeatureRenderer(data, false);
}
});
this.add(tabbedPane, java.awt.BorderLayout.CENTER);
- tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
- tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
+ settingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.das_settings"),
+ dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transbuttons.add(optimizeOrder);
transbuttons.add(invert);
this.data = data;
}
- private String[] columnNames =
- { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
+ private String[] columnNames = {
+ MessageManager.getString("label.feature_type"),
+ MessageManager.getString("action.colour"),
+ MessageManager.getString("label.display") };
private Object[][] data;
*/
package jalview.gui;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.Vector;
import javax.swing.JOptionPane;
import javax.swing.KeyStroke;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GFinder;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
/**
* Performs the menu option for searching the alignment, for the next or all
* matches. If matches are found, they are highlighted, and the user has the
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.jbgui.GFontChooser;
+import jalview.util.MessageManager;
+
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.event.ActionEvent;
import javax.swing.JLayeredPane;
import javax.swing.JOptionPane;
-import jalview.bin.Cache;
-import jalview.jbgui.GFontChooser;
-import jalview.util.MessageManager;
-
/**
* DOCUMENT ME!
*
{
final String messageKey = iBounds.getHeight() < 1 ? "label.font_doesnt_have_letters_defined"
: "label.font_too_small";
- JOptionPane
- .showInternalMessageDialog(
- this,
+ JOptionPane.showInternalMessageDialog(this,
MessageManager.getString(messageKey),
- MessageManager.getString("label.invalid_font"), JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.invalid_font"),
+ JOptionPane.WARNING_MESSAGE);
/*
* Restore the changed value - note this will reinvoke this method via the
* ActionListener, but now validation should pass
bg.add(text);
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[]
- { this });
+ JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options");
dialog.setVisible(true);
*
* This is a workaround for issue JAL-914 - both Desktop and AlignFrame
* responding to F1 key, resulting in duplicate help windows opened.
- * @param id TODO
+ *
+ * @param id
+ * TODO
*
* @throws HelpSetException
*/
* DOCUMENT ME!
*/
public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
- int i, int starty,
- int ypos)
+ int i, int starty, int ypos)
{
int xPos = 0;
int panelWidth = getWidth();
if (below)
{
gg.fillPolygon(
- new int[]
- { getWidth() - av.getCharHeight(),
- getWidth() - av.getCharHeight(),
- getWidth() }, new int[]
- {
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
(i - starty) * av.getCharHeight() + yoffset,
(i - starty) * av.getCharHeight() + yoffset
+ av.getCharHeight() / 4,
if (above)
{
gg.fillPolygon(
- new int[]
- { getWidth() - av.getCharHeight(),
- getWidth() - av.getCharHeight(),
- getWidth() }, new int[]
- {
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
(i - starty + 1) * av.getCharHeight() + yoffset,
(i - starty + 1) * av.getCharHeight() + yoffset
- av.getCharHeight() / 4,
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
StringBuffer tip = new StringBuffer(64);
- seqAnnotReport
- .createSequenceAnnotationReport(tip, sequence,
+ seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
av.isShowDBRefs(), av.isShowNPFeats(),
- sp.seqCanvas.fr.getMinMax());
+ sp.seqCanvas.fr.getMinMax());
setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+ tip.toString() + "</html>");
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Image;
import javax.swing.JPanel;
-import jalview.api.AlignViewportI;
-
/**
* DOCUMENT ME!
*
public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
{
- initDialogFrame(this, true, false, MessageManager.getString("label.select_database_retrieval_source"),
+ initDialogFrame(this, true, false,
+ MessageManager
+ .getString("label.select_database_retrieval_source"),
650, 490);
/*
* Dynamically generated database list will need a translation function from
}
else
{
- throw new Error(MessageManager.getString("error.implementation_error_cant_reorder_tree"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cant_reorder_tree"));
}
}
jalview.util.QuickSort.sort(names, nodes);
if (allowMultiSelections)
{
dbstatus.setText(MessageManager.formatMessage(
- "label.selected_database_to_fetch_from", new String[]
- {
+ "label.selected_database_to_fetch_from", new String[] {
Integer.valueOf(srcs.size()).toString(),
(srcs.size() == 1 ? "" : "s"),
(srcs.size() > 0 ? " with " + x + " test quer"
if (nm.length() > 0)
{
dbstatus.setText(MessageManager.formatMessage(
- "label.database_param", new String[]
- { nm }));
+ "label.database_param", new String[] { nm }));
if (qr.length() > 0)
{
dbstatex.setText(MessageManager.formatMessage(
- "label.example_param", new String[]
- { qr }));
+ "label.example_param", new String[] { qr }));
}
else
{
}
}
throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam", new Object[]
- { calcIdParam.toString() }));
+ "error.unsupported_version_calcIdparam",
+ new Object[] { calcIdParam.toString() }));
}
/**
else
{
// defer to later
- frefedSequence.add(new Object[]
- { maps[m].getDnasq(), cf, mapping });
+ frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+ mapping });
}
}
}
/**
* Kludge for magic autoannotation names (see JAL-811)
*/
- String[] magicNames = new String[]
- { "Consensus", "Quality", "Conservation" };
+ String[] magicNames = new String[] { "Consensus", "Quality",
+ "Conservation" };
JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
for (String nm : magicNames)
}
else
{
- frefedSequence.add(new Object[]
- { dsfor, jmap });
+ frefedSequence.add(new Object[] { dsfor, jmap });
}
}
else
+ "\n");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new String[]
- { file }), MessageManager
+ new String[] { file }), MessageManager
.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
}
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
+ MessageManager.formatMessage(
+ "label.error_loading_file_params", new String[]
+ { file }), MessageManager
+ .getString("label.error_loading_jalview_file"),
JOptionPane.WARNING_MESSAGE);
}
});
for (int s = 0; s < ids.length; s++)
{
- seqs.addElement(seqids
- .elementAt(ids[s]));
+ seqs.addElement(seqids.elementAt(ids[s]));
}
jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
- featureColours.put(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(),
+ new java.awt.Color(setting.getColour()));
renderOrder[fs] = setting.getType();
if (setting.getDisplay())
{
- featuresDisplayed.put(setting.getType(), new Integer(
- setting.getColour()));
+ featuresDisplayed.put(setting.getType(),
+ new Integer(setting.getColour()));
}
}
- FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, new Hashtable(), featureColours, 1.0f, null);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
}
af.setMenusFromViewport(af.viewport);
}
@Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
: (AlignmentPanel) alignment;
@Override
public void run()
{
- long stm = cvf.startProgressBar(progressMsg);
- try
- {
- sendChimeraCommand(command, false);
- } finally
- {
- cvf.stopProgressBar(null, stm);
- }
+ long stm = cvf.startProgressBar(progressMsg);
+ try
+ {
+ sendChimeraCommand(command, false);
+ } finally
+ {
+ cvf.stopProgressBar(null, stm);
+ }
}
});
- thread.start();
+ thread.start();
}
}
return enclose ? "<html>" + ttext + "</html>" : ttext;
}
- return (enclose ? "<html>" : "")
- + "<style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
- + ttext + "</p>" + ((enclose ? "</html>" : ""));
+ return (enclose ? "<html>" : "")
+ + "<style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
+ + ttext + "</p>" + ((enclose ? "</html>" : ""));
}
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- desktop,
- MessageManager.formatMessage("warn.out_of_memory_when_action", new String[]{action}),
- MessageManager.getString("label.out_of_memory"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ javax.swing.JOptionPane.showInternalMessageDialog(desktop,
+ MessageManager.formatMessage("warn.out_of_memory_when_action",
+ new String[] { action }), MessageManager
+ .getString("label.out_of_memory"),
+ javax.swing.JOptionPane.WARNING_MESSAGE);
// hope that there's enough memory left that no more appear.
oomInprogress = false;
}
import java.awt.event.MouseListener;
import java.net.URL;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
{
hasLink = true;
- enabled.setToolTipText(
- JvSwingUtils
- .wrapTooltip(true, ((desc == null || desc.trim().length() == 0) ? MessageManager.getString("label.opt_and_params_further_details ")
+ enabled.setToolTipText(JvSwingUtils
+ .wrapTooltip(
+ true,
+ ((desc == null || desc.trim().length() == 0) ? MessageManager
+ .getString("label.opt_and_params_further_details ")
: desc)
- + "<br><img src=\"" + linkImageURL + "\"/>")
- );
+ + "<br><img src=\"" + linkImageURL + "\"/>"));
enabled.addMouseListener(this);
}
else
{
if (desc != null && desc.trim().length() > 0)
{
- enabled.setToolTipText(
- JvSwingUtils.wrapTooltip(true, opt.getDescription())
- );
+ enabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ opt.getDescription()));
}
}
add(enabled, BorderLayout.NORTH);
{
// Only create description boxes if there actually is a description.
ttipText = (JvSwingUtils
- .wrapTooltip(true, parm.getDescription()
+ .wrapTooltip(
+ true,
+ parm.getDescription()
+ (finfo != null ? "<br><img src=\""
+ linkImageURL
- + "\"/>"+MessageManager.getString("label.opt_and_params_further_detail")
+ + "\"/>"
+ + MessageManager
+ .getString("label.opt_and_params_further_detail")
: "")));
}
// Only create description boxes if there actually is a description.
if (finfo != null)
{
- showDesc.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.opt_and_params_show_brief_desc_image_link", new String[]{linkImageURL.toExternalForm()})));
+ showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ MessageManager
+ .formatMessage(
+ "label.opt_and_params_show_brief_desc_image_link",
+ new String[] { linkImageURL
+ .toExternalForm() })));
showDesc.addMouseListener(this);
}
else
{
- showDesc.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.opt_and_params_show_brief_desc")));
+ showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ MessageManager
+ .getString("label.opt_and_params_show_brief_desc")));
}
showDesc.addActionListener(new ActionListener()
{
{
slider.setVisible(false);
}
- return new int[]
- { iVal };
+ return new int[] { iVal };
}
else
{
{
slider.setVisible(false);
}
- return new float[]
- { fVal };
+ return new float[] { fVal };
}
}
else
if (!choice)
{
slider.setVisible(false);
- return new String[]
- { valueField.getText().trim() };
+ return new String[] { valueField.getText().trim() };
}
else
{
- return new String[]
- { (String) choicebox.getSelectedItem() };
+ return new String[] { (String) choicebox.getSelectedItem() };
}
}
JPopupMenu mnu = new JPopupMenu();
JMenuItem mitem = new JMenuItem(MessageManager.formatMessage(
- "label.view_params", new String[]
- { finfo }));
+ "label.view_params", new String[] { finfo }));
mitem.addActionListener(new ActionListener()
{
}
else
{
- throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option.getName()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.invalid_value_for_option", new String[] { string,
+ option.getName() }));
}
}
sr.renderGaps = false;
sr.forOverview = true;
fr = new FeatureRenderer(ap);
-
+
// scale the initial size of overviewpanel to shape of alignment
float initialScale = (float) av.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
}
if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = new Color(color).darker().darker().getRGB();
}
*/
package jalview.gui;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Graphics;
import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.PCAModel;
-
/**
* DOCUMENT ME!
*
if (!sameLength)
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.pca_sequences_not_aligned"),
+ MessageManager.getString("label.sequences_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
public void bgcolour_actionPerformed(ActionEvent e)
{
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_backgroud_colour"),
rc.bgColour);
if (col != null)
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params", new String[]
- { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params",
+ new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
- "Make PNG image from PCA", width, height, null, null);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
+ width, height, null, null);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
- "Make EPS file from PCA", width, height, null,
- this.getTitle());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
+ width, height, null, this.getTitle());
}
else
{
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.points_for_params", new String[]
- { this.getTitle() }), 500, 500);
+ "label.points_for_params", new String[] { this.getTitle() }),
+ 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.transformed_points_for_params", new String[]
- { this.getTitle() }), 500, 500);
+ "label.transformed_points_for_params",
+ new String[] { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
cap.dispose();
}
}
+
/*
* (non-Javadoc)
*
.getProgressIndicator();
}
-
/**
* Action performed when an input is detected on txt_search field.
*/
return foundSearchTerms;
}
-
@Override
public void btn_ok_ActionPerformed()
{
JMenuItem sequenceDetails = new JMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
-
+
JMenuItem makeReferenceSeq = new JMenuItem();
JMenuItem chooseAnnotations = new JMenuItem();
{
makeReferenceSeq.setText(MessageManager
.getString("action.unmark_as_reference"));
- } else {
+ }
+ else
+ {
makeReferenceSeq.setText(MessageManager
.getString("action.set_as_reference"));
}
*/
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new Object[]
- { aa.label }));
+ "label.2d_rna_structure_line",
+ new Object[] { aa.label }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name", new Object[]
- { seq.getName() }));
+ "label.2d_rna_sequence_name",
+ new Object[] { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { seq.getName() }));
+ "label.represent_group_with",
+ new Object[] { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new Object[]
- { sg.getName() }));
+ new Object[] { sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- { urlLink.getTarget() });
+ seq.getDBRef(), new String[] { urlLink.getTarget() });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
*/
Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
- AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
- hiddenTypes,
- AlignmentAnnotationUtils.asList(annotations),
- forSequences);
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
for (String calcId : hiddenTypes.keySet())
{
for (List<String> type : hiddenTypes.get(calcId))
{
- addAnnotationTypeToShowHide(showMenu, forSequences,
- calcId, type, false, true);
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
}
}
// grey out 'show annotations' if none are hidden
{
for (List<String> type : shownTypes.get(calcId))
{
- addAnnotationTypeToShowHide(hideMenu, forSequences,
- calcId, type, false, false);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
}
}
// grey out 'hide annotations' if none are shown
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
- forSequences, allTypes, actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
refresh();
}
});
// ID/regex match URLs
groupLinksMenu = new JMenu(
MessageManager.getString("action.group_link"));
- JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")),
+ JMenu[] linkMenus = new JMenu[] { null,
+ new JMenu(MessageManager.getString("action.ids")),
new JMenu(MessageManager.getString("action.sequences")),
new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
// types
if (sarray == null)
{
sarray = new Object[2];
- sarray[0] = new int[]
- { 0 };
+ sarray[0] = new int[] { 0 };
sarray[1] = new String[seqs.length];
commonDbrefs.put(src, sarray);
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_param", new Object[]
- { url }));
+ "label.open_url_param", new Object[] { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
"label.open_url_seqs_param",
- new Object[]
- { urlgenerator.getUrl_prefix(),
+ new Object[] { urlgenerator.getUrl_prefix(),
urlgenerator.getNumberInvolved(urlstub) }));
// TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { sequence };
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
if (ap.av.getSelectionGroup() != null)
{
selectedSeqs = ap.av.getSequenceSelection();
.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent actionEvent)
{
makeReferenceSeq_actionPerformed(actionEvent);
-
+
}
});
- hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
+ hideInsertions.setText(MessageManager
+ .getString("label.hide_insertions"));
hideInsertions.addActionListener(new ActionListener()
{
add(sequenceMenu);
add(rnaStructureMenu);
add(pdbStructureDialog);
- if (sequence!=null)
+ if (sequence != null)
{
add(hideInsertions);
}
* @param menuItem
* @param forSequences
*/
- protected void configureReferenceAnnotationsMenu(
- JMenuItem menuItem, List<SequenceI> forSequences)
+ protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+ List<SequenceI> forSequences)
{
menuItem.setEnabled(false);
}
refresh();
}
+
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
protected void sequenceDetails_actionPerformed()
{
- createSequenceDetailsReport(new SequenceI[]
- { sequence });
+ createSequenceDetailsReport(new SequenceI[] { sequence });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
+ MessageManager
.formatMessage(
"label.create_sequence_details_report_annotation_for",
- new Object[]
- { seq.getDisplayId(true) }) + "</h2></p><p>");
+ new Object[] { seq.getDisplayId(true) })
+ + "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
true,
false,
(ap.getSeqPanel().seqCanvas.fr != null) ? ap
- .getSeqPanel().seqCanvas.fr
- .getMinMax()
+ .getSeqPanel().seqCanvas.fr.getMinMax()
: null);
contents.append("</p>");
}
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.sequence_details_for",
- (sequences.length == 1 ? new Object[]
- { sequences[0].getDisplayId(true) } : new Object[]
- { MessageManager.getString("label.selection") })), 500, 400);
+ (sequences.length == 1 ? new Object[] { sequences[0]
+ .getDisplayId(true) } : new Object[] { MessageManager
+ .getString("label.selection") })), 500, 400);
}
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null || sg.getSize() < 1)
{
- ap.av.hideSequence(new SequenceI[]
- { sequence });
+ ap.av.hideSequence(new SequenceI[] { sequence });
return;
}
if (sg != null)
{
List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
- sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new Object[]
- { sequence.getDisplayId(false) }));
+ "label.select_pdb_file_for",
+ new Object[] { sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new Object[]
- { sequence.getDisplayId(false) }));
+ "label.load_pdb_file_associate_with_sequence",
+ new Object[] { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
}
-
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
sortAutocalc.addItem("Autocalculated first");
sortAutocalc.addItem("Autocalculated last");
- final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
- true);
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
: sortAutocalc.getItemAt(1));
startupCheckbox
structFromPdb.setSelected(structSelected);
useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
useRnaView.setEnabled(structSelected);
- addSecondaryStructure
- .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
- Boolean.valueOf(showAutocalcFirst).toString());
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
return validateChimeraPath();
}
+
/**
* DOCUMENT ME!
*/
public void startupFileTextfield_mouseClicked()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
- new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+ "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
+ "PIR", "BLC", "Jalview" },
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
public void minColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
panel.setBackground(col);
public void maxColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
panel.setBackground(col);
}
} catch (NumberFormatException x)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("warn.user_defined_width_requirements"),
- MessageManager.getString("label.invalid_id_column_width"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
}
}
if (!found)
{
- String[] options =
- { "OK", "Help" };
+ String[] options = { "OK", "Help" };
int showHelp = JOptionPane.showInternalOptionDialog(
Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
- "", JOptionPane.YES_NO_OPTION,
- JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+ "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
if (showHelp == JOptionPane.NO_OPTION)
{
try
public void setProgressBar(String message, long id)
{
Long longId = Long.valueOf(id);
-
+
JPanel progressPanel = progressBars.get(longId);
if (progressPanel != null)
{
* No progress bar for this id - add one now
*/
progressPanel = new JPanel(new BorderLayout(10, 5));
-
+
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
-
+
progressPanel.add(new JLabel(message), BorderLayout.WEST);
progressPanel.add(progressBar, BorderLayout.CENTER);
-
+
addRow(progressPanel);
-
+
progressBars.put(longId, progressPanel);
}
{
handler.cancelActivity(id);
us.setProgressBar(MessageManager.formatMessage(
- "label.cancelled_params", new Object[]
- { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
+ "label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0))
+ .getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
import java.awt.Component;
-import javax.swing.*;
+import javax.swing.JOptionPane;
public class PromptUserConfig implements Runnable
{
progress.setVisible(false);
progress = null;
- label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_thereshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
}
}
- EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
Action.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
*/
public void undoButton_actionPerformed(ActionEvent e)
{
- if(historyList == null || historyList.isEmpty()){
- undoButton.setEnabled(false);
- return;
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
}
-
+
CommandI command = historyList.pop();
if (ap.av.getHistoryList().contains(command))
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
af.updateEditMenuBar();
}
*/
package jalview.gui;
+import jalview.jbgui.GRestInputParamEditDialog;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestServiceDescription;
+
import java.util.ArrayList;
import java.util.Hashtable;
import net.miginfocom.swing.MigLayout;
-import jalview.jbgui.GRestInputParamEditDialog;
-import jalview.ws.params.InvalidArgumentException;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.RestServiceDescription;
-
public class RestInputParamEditDialog extends GRestInputParamEditDialog
implements OptsParametersContainerI
{
parseRes.setText(MessageManager
.formatMessage(
"label.parsing_failed_syntax_errors_shown_below_param",
- new String[]
- { rsd.getInvalidMessage() }));
+ new String[] { rsd.getInvalidMessage() }));
parseWarnings.setVisible(true);
}
} catch (Throwable e)
parseRes.setText(MessageManager
.formatMessage(
"label.parsing_failed_unrecoverable_exception_thrown_param",
- new String[]
- { e.toString() }));
+ new String[] { e.toString() }));
parseWarnings.setVisible(true);
}
}
*/
package jalview.gui;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
/**
* DOCUMENT ME!
*
}
else
{
- return new AlignmentPanel[]
- { ap };
+ return new AlignmentPanel[] { ap };
}
}
bg.add(text);
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[]
- { this });
+ JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options");
dialog.setVisible(true);
gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
y + 2,
- ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
- y + (fm.getDescent() * 2));
+ ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
+ + (fm.getDescent() * 2));
}
else
{
- gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
- y + fm.getDescent(), ((i - startx - 1) * avCharWidth)
+ gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
+ + fm.getDescent(), ((i - startx - 1) * avCharWidth)
+ (avCharWidth / 2), y + (fm.getDescent() * 2));
}
}
continue;
}
- gg.fillPolygon(new int[]
- { res * avCharWidth - avCharHeight / 4,
+ gg.fillPolygon(new int[] { res * avCharWidth - avCharHeight / 4,
res * avCharWidth + avCharHeight / 4, res * avCharWidth },
- new int[]
- { y - avCharHeight / 2, y - avCharHeight / 2, y + 8 },
- 3);
+ new int[] { y - avCharHeight / 2, y - avCharHeight / 2,
+ y + 8 }, 3);
}
}
charHeight = av.getCharHeight();
charWidth = av.getCharWidth();
}
+
/**
* DOCUMENT ME!
*
g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
(ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
- + (charWidth / 2),
- ypos - 2);
+ + (charWidth / 2), ypos - 2);
}
}
continue;
}
- gg.fillPolygon(new int[]
- { res * charWidth - charHeight / 4,
- res * charWidth + charHeight / 4, res * charWidth },
- new int[]
- { ypos - (charHeight / 2), ypos - (charHeight / 2),
- ypos - (charHeight / 2) + 8 }, 3);
+ gg.fillPolygon(
+ new int[] { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[] { ypos - (charHeight / 2),
+ ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ 3);
}
}
annotations = new AnnotationPanel(av);
}
- annotations.renderer.drawComponent(annotations, av, g,
- -1, startRes, endx + 1);
+ annotations.renderer.drawComponent(annotations, av, g, -1,
+ startRes, endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
* DOCUMENT ME!
*/
public void drawPanel(Graphics g1, int startRes, int endRes,
- int startSeq,
- int endSeq, int offset)
+ int startSeq, int endSeq, int offset)
{
updateViewport();
if (!av.hasHiddenColumns())
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// int x1, int x2, int y1, int y2, int startx, int starty,
private void draw(Graphics g, int startRes, int endRes, int startSeq,
- int endSeq,
- int offset)
+ int endSeq, int offset)
{
g.setFont(av.getFont());
sr.prepare(g, av.isRenderGaps());
if (group == av.getSelectionGroup())
{
g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+ 0f));
g.setColor(Color.RED);
}
else
break;
}
- group = av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
y -= hgap;
@Override
public void highlightSequence(SearchResults results)
{
- if (results == null || results.equals(lastSearchResults)) {
+ if (results == null || results.equals(lastSearchResults))
+ {
return;
}
lastSearchResults = results;
-
+
if (av.isFollowHighlight())
{
/*
{
return this.ap == null ? null : this.ap.av;
}
+
@Override
public void updateColours(SequenceI seq, int index)
{
if (av.isShowSequenceFeatures())
{
int rpos;
- List<SequenceFeature> features = ap.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(),
- rpos = sequence.findPosition(res));
+ List<SequenceFeature> features = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
seqARep.appendFeatures(tooltipText, rpos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[] { label }));
}
}
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- appendEdit(Action.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres);
+ appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
else
endEditing();
break;
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
}
}
else
if (max > 0)
{
- appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seq }, startres, max);
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
}
}
}
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- appendEdit(Action.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres);
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
}
final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
av.getAlignment().getGapCharacter());
- editCommand.appendEdit(edit, av.getAlignment(),
- true, null);
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
av.setSelectionGroup(null);
}
- List<SequenceFeature> features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
- if (features != null && features.size()> 0)
+ if (features != null && features.size() > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(),
- features.get(0).getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
}
- if (features != null && features.size()> 0)
+ if (features != null && features.size() > 0)
{
- seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
+ seqCanvas.getFeatureRenderer().amendFeatures(
+ new SequenceI[] { sequence },
+ features.toArray(new SequenceFeature[features.size()]),
+ false, ap);
seqCanvas.highlightSearchResults(null);
}
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- List<SequenceFeature> allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
+ List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(res));
Vector links = new Vector();
- for (SequenceFeature sf:allFeatures)
+ for (SequenceFeature sf : allFeatures)
{
if (sf.links != null)
{
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- boolean iSentTheSelection = (av == source
- || (source instanceof AlignViewport && ((AlignmentViewport) source)
+ boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())));
if (iSentTheSelection || !av.followSelection)
{
protected boolean selectionFromTranslation(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
- if (!(source instanceof AlignViewportI)) {
+ if (!(source instanceof AlignViewportI))
+ {
return false;
}
final AlignViewportI sourceAv = (AlignViewportI) source;
- if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
{
return false;
}
private static Thread initingThread = null;
int debounceTrap = 0;
+
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
{
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow
+ .setProgressBar(
+ MessageManager
+ .getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
// finishes.
}
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow
+ .setProgressBar(
+ MessageManager
+ .getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
}
if (sfetch == null
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+ guiWindow.setProgressBar(MessageManager
+ .getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
}
private IProgressIndicator progressIndicator;
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
this.progressIndicator = guiIndic;
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager.getString("label.couldnt_create_sequence_fetcher"),
+ MessageManager
+ .getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager
+ .getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
private String getFrameTitle()
{
- return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
+ return ((alignFrame == null) ? MessageManager
+ .getString("label.new_sequence_fetcher") : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
String currentSelection = database.getSelectedItem();
if (!currentSelection.equalsIgnoreCase("pdb"))
{
- otherSourceAction();
+ otherSourceAction();
}
if (currentSelection.equalsIgnoreCase("pdb")
&& (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
: ""));
String eq = database.getExampleQueries();
dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[]
- { eq }));
+ "label.example_query_param", new String[] { eq }));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
jPanel3.repaint();
}
-
-
public void close_actionPerformed(ActionEvent e)
{
try
try
{
// update status
- guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
- .currentThread().hashCode());
+ guiWindow
+ .setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from",
+ new String[] {
+ Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }), Thread.currentThread()
+ .hashCode());
isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
if (proxy.getAccessionSeparator() == null)
{
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+ guiWindow.setProgressBar(MessageManager
+ .getString("status.finshed_querying"), Thread.currentThread()
.hashCode());
}
- guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
- : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ (presult.size() > 0) ? MessageManager
+ .getString("status.parsing_results") : MessageManager
+ .getString("status.processing"), Thread.currentThread()
+ .hashCode());
// process results
while (presult.size() > 0)
{
return progressIndicator;
}
-
-
public void setProgressIndicator(IProgressIndicator progressIndicator)
{
this.progressIndicator = progressIndicator;
int y1)
{
if (seq == null)
- {
+ {
return; // fix for racecondition
}
int i = start;
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s),
- charOffset + av.getCharWidth()
- * (i - start), y1);
+ charOffset + av.getCharWidth() * (i - start), y1);
}
}
sp.cs = cs;
}
- conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
+ conservationSlider
+ .setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
{
pid.cs = cs;
}
- PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+ PIDSlider.setTitle(MessageManager
+ .formatMessage("label.percentage_identity_thereshold",
+ new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
{
adjustLayout();
addCloseFrameListener();
-
+
addKeyListener();
addKeyBindings();
*/
protected void addKeyListener()
{
- addKeyListener(new KeyAdapter() {
+ addKeyListener(new KeyAdapter()
+ {
@Override
public void keyPressed(KeyEvent e)
}
}
}
-
+
});
}
overrideKeyBinding(key_cmdF, action);
}
}
-
private boolean isValidPBDEntry;
-
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
if (seq.getDatasetSequence() != null
&& seq.getDatasetSequence().getAllPDBEntries() != null)
{
- for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
+ for (PDBEntry pdbEntry : seq.getDatasetSequence()
+ .getAllPDBEntries())
{
if (pdbEntry.getFile() != null)
{
tbl_local_pdb.setModel(tableModelx);
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
// Update table selection model here
tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time",
- totalTime));
+ "label.structure_chooser_filter_time", totalTime));
}
else
{
mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time",
- totalTime));
+ "label.structure_chooser_filter_time", totalTime));
if (errors.size() > 0)
{
StringBuilder errorMsg = new StringBuilder();
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(null, errorMsg.toString(),
+ JOptionPane.showMessageDialog(
+ null,
+ errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
JOptionPane.ERROR_MESSAGE);
}
lbl_pdbManualFetchStatus.setToolTipText("");
if (txt_search.getText().length() > 0)
{
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, MessageManager.formatMessage(
- "info.no_pdb_entry_found_for",
+ lbl_pdbManualFetchStatus
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .formatMessage("info.no_pdb_entry_found_for",
txt_search.getText())));
}
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}
- PDBEntry[] pdbEntriesToView = new PDBEntry[]
- { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, new SequenceI[]
- { selectedSequence });
+ pdbEntriesToView, ap, new SequenceI[] { selectedSequence });
}
else if (currentView == VIEWS_FROM_FILE)
{
selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
- new PDBEntry[]
- { fileEntry }, ap, new SequenceI[]
- { selectedSequence });
+ new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[] { selectedSequence });
}
mainFrame.dispose();
}
ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
for (SequenceI seq : sequences)
{
- seqsMap.add(new SequenceI[]
- { seq });
+ seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
{
public void run()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
- {
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
validateSelections();
}
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
- }
- }
- validateSelections();
- }
}.start();
}
public class PDBEntryTableModel extends AbstractTableModel
{
- String[] columns =
- { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
private List<CachedPDB> pdbEntries;
*/
package jalview.gui;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.StructureViewerModel;
import jalview.structure.StructureSelectionManager;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* proxy for handling structure viewers.
*
* @return
*/
private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
- SequenceI[][] seqsForPdbs,
- AlignmentPanel ap)
+ SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
List<SequenceI> seqs = new ArrayList<SequenceI>();
if (pdbs == null || pdbs.length == 0)
*/
public JalviewStructureDisplayI createView(ViewerType type,
String[] pdbf, String[] id, SequenceI[][] sq,
- AlignmentPanel alignPanel, StructureViewerModel viewerData, String fileloc,
- Rectangle rect, String vid)
+ AlignmentPanel alignPanel, StructureViewerModel viewerData,
+ String fileloc, Rectangle rect, String vid)
{
final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
* list of sequenceSet ids associated with the view
*/
protected List<String> _aps = new ArrayList<String>();
+
/**
* list of alignment panels to use for superposition
*/
protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
private String viewId = null;
+
private AlignmentPanel ap;
+
protected boolean alignAddedStructures = false;
+
protected boolean _started = false;
+
protected boolean addingStructures = false;
+
protected Thread worker = null;
/**
public boolean isUsedforaligment(AlignmentPanel ap2)
{
-
+
return (_alignwith != null) && _alignwith.contains(ap2);
}
list = t;
}
}
-
+
return list;
}
}
}
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
{
useAlignmentPanelForColourbyseq(nap);
getBinding().setColourBySequence(enableColourBySeq);
* alignment
* @param alignFrame
*/
- protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains,
+ protected void addStructure(final PDBEntry pdbentry,
+ final SequenceI[] seqs, final String[] chains,
final boolean align, final IProgressIndicator alignFrame)
{
if (pdbentry.getFile() == null)
try
{
Thread.sleep(100 + ((int) Math.random() * 100));
-
+
} catch (Exception e)
{
}
* @param view
* @return YES, NO or CANCEL JOptionPane code
*/
- protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view)
+ protected int chooseAlignStructureToViewer(String pdbId,
+ StructureViewerBase view)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbId, view.getTitle() }), MessageManager
+ new Object[] { pdbId, view.getTitle() }),
+ MessageManager
.getString("label.align_to_existing_structure_view"),
JOptionPane.YES_NO_CANCEL_OPTION);
return option;
// NO_OPTION - offer the next viewer if any
}
}
-
+
/*
* nothing offered and selected
*/
/*
* create the mappings
*/
- apanel.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
- AppletFormatAdapter.FILE);
-
+ apanel.getStructureSelectionManager().setMapping(seq, chains,
+ pdbFilename, AppletFormatAdapter.FILE);
+
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
*/
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
apanel.paintAlignment(true);
}
-
+
/*
* add the sequences to any other viewers (of the same type) for this pdb
* file
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(apanel);
+ apanel.getStructureSelectionManager().sequenceColoursChanged(
+ apanel);
break;
}
}
boolean finished = false;
String alreadyMapped = apanel.getStructureSelectionManager()
.alreadyMappedToFile(pdbId);
-
+
if (alreadyMapped != null)
{
/*
* the PDB file is already loaded
*/
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbId }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed",
+ new Object[] { pdbId }), MessageManager
+ .formatMessage(
+ "label.map_sequences_to_visible_window",
+ new Object[] { pdbId }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
if (option == JOptionPane.CANCEL_OPTION)
{
finished = true;
JPanel panel = new JPanel();
bigpanel.add(panel, BorderLayout.CENTER);
bigpanel.add(
- new JLabel("<html>"+MessageManager.getString("label.select_dark_light_set_thereshold")+"</html>"),
- BorderLayout.NORTH);
+ new JLabel(
+ "<html>"
+ + MessageManager
+ .getString("label.select_dark_light_set_thereshold")
+ + "</html>"), BorderLayout.NORTH);
panel.add(col1);
panel.add(slider);
panel.add(col2);
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
- MessageManager.getString("label.select_colour_for_text"), col1.getBackground());
+ MessageManager.getString("label.select_colour_for_text"),
+ col1.getBackground());
if (col != null)
{
colour1Changed(col);
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
- MessageManager.getString("label.select_colour_for_text"), col2.getBackground());
+ MessageManager.getString("label.select_colour_for_text"),
+ col2.getBackground());
if (col != null)
{
colour2Changed(col);
}
});
- int reply = JOptionPane.showInternalOptionDialog(ap, bigpanel,
- MessageManager.getString("label.adjunst_foreground_text_colour_thereshold"),
- JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
- null, null, null);
+ int reply = JOptionPane
+ .showInternalOptionDialog(
+ ap,
+ bigpanel,
+ MessageManager
+ .getString("label.adjunst_foreground_text_colour_thereshold"),
+ JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, null, null);
if (reply == JOptionPane.CANCEL_OPTION)
{
SequenceGroup selected = av.getSelectionGroup();
if ((selected != null)
- && selected.getSequences(null).contains(
- node.element()))
+ && selected.getSequences(null).contains(node.element()))
{
g.setColor(Color.gray);
labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
- float wscale = (width - labelLength - (offx * 2))
- / tree.getMaxHeight();
+ float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
if (SwingUtilities.isRightMouseButton(evt))
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"), highlightNode.color);
+ MessageManager.getString("label.select_subtree_colour"),
+ highlightNode.color);
if (col != null)
{
setColor(highlightNode, col);
if (av.getCodingComplement() != null)
{
- ((AlignViewport) av.getCodingComplement()).getAlignPanel().updateAnnotation();
+ ((AlignViewport) av.getCodingComplement()).getAlignPanel()
+ .updateAnnotation();
/*
* idPanel. repaint ()
*/
}
else
{
- return new AlignmentPanel[]
- { ap };
+ return new AlignmentPanel[] { ap };
}
}
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params", new Object[]
- { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params",
+ new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "eps" }, new String[]
- { "Encapsulated Postscript" }, "Encapsulated Postscript");
+ { "eps" }, new String[] { "Encapsulated Postscript" },
+ "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "png" }, new String[]
- { "Portable network graphics" }, "Portable network graphics");
+ { "png" }, new String[] { "Portable network graphics" },
+ "Portable network graphics");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
// search dbrefs, features and annotation
DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRef(), new String[]
- { labelClass.toUpperCase() });
+ sq.getDBRef(),
+ new String[] { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
*/
package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
import java.awt.Color;
import java.awt.Font;
import java.awt.event.ActionEvent;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.datamodel.SequenceGroup;
-import jalview.io.JalviewFileChooser;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
/**
* This panel allows the user to assign colours to Amino Acid residue codes, and
* save the colour scheme.
|| upperCaseButtons.isEmpty();
final boolean noLowerCaseSelected = caseSensitive.isSelected()
&& (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
- final boolean noSelectionMade = noUpperCaseSelected || noLowerCaseSelected;
+ final boolean noSelectionMade = noUpperCaseSelected
+ || noLowerCaseSelected;
return noSelectionMade;
}
{
if (isNoSelectionMade())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
- JOptionPane.WARNING_MESSAGE);
-
- }
- UserColourScheme ucs = getSchemeFromButtons();
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JOptionPane.WARNING_MESSAGE);
+
+ }
+ UserColourScheme ucs = getSchemeFromButtons();
ucs.setName(schemeName.getText());
if (seqGroup != null)
Color[] newColours = new Color[24];
int length = upperCaseButtons.size();
- if (length<24){
- int i = 0;
- for (JButton btn:upperCaseButtons){
- newColours[i] = btn.getBackground();
- i++;
- }
- }else{
- for (int i = 0; i < 24; i++){
- JButton button = upperCaseButtons.get(i);
- newColours[i] = button.getBackground();
- }
+ if (length < 24)
+ {
+ int i = 0;
+ for (JButton btn : upperCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 24; i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
}
UserColourScheme ucs = new UserColourScheme(newColours);
{
newColours = new Color[23];
length = lowerCaseButtons.size();
- if (length<23){
- int i = 0;
- for (JButton btn:lowerCaseButtons){
- newColours[i] = btn.getBackground();
- i++;
- }
- }else{
- for (int i = 0; i < 23; i++){
- JButton button = lowerCaseButtons.get(i);
- newColours[i] = button.getBackground();
- }
+ if (length < 23)
+ {
+ int i = 0;
+ for (JButton btn : lowerCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 23; i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
}
ucs.setLowerCaseColours(newColours);
}
lowerCaseButtons = new ArrayList<JButton>();
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jc" }, new String[]
- { "Jalview User Colours" }, "Jalview User Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "jc" }, new String[] { "Jalview User Colours" },
+ "Jalview User Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.load_colour_scheme"));
name = jucs.getColour(i).getName();
if (ResidueProperties.aa3Hash.containsKey(name))
{
- index = ResidueProperties.aa3Hash.get(name)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(name).intValue();
}
else
{
{
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.colour_scheme_exists_overwrite", new Object[]
- { schemeName.getText(), schemeName.getText() }),
+ "label.colour_scheme_exists_overwrite", new Object[] {
+ schemeName.getText(), schemeName.getText() }),
MessageManager.getString("label.duplicate_scheme_name"),
JOptionPane.YES_NO_OPTION);
if (reply != JOptionPane.YES_OPTION)
userColourSchemes.remove(schemeName.getText());
}
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jc" }, new String[]
- { "Jalview User Colours" }, "Jalview User Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "jc" }, new String[] { "Jalview User Colours" },
+ "Jalview User Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
import jalview.util.MessageManager;
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
-import javax.swing.*;
+import javax.swing.JOptionPane;
public class UserQuestionnaireCheck implements Runnable
{
{
if (sess != null)
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
.showInternalMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
- MessageManager.getString("label.vamsas_document_import_failed"),
+ MessageManager
+ .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
{
if (!inSession())
{
- throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
{
if (!inSession())
{
- throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+ throw new Error(
+ MessageManager
+ .getString("error.jalview_no_connected_vamsas_session"));
}
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
return;
}
- throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
if (source instanceof AlignViewport)
{
// the empty selection.
- sm = new SelectionMessage("jalview", new String[]
- { ((AlignmentViewport) source).getSequenceSetId() }, null,
- true);
+ sm = new SelectionMessage("jalview",
+ new String[] { ((AlignmentViewport) source)
+ .getSequenceSetId() }, null, true);
}
else
{
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import jalview.util.MessageManager;
-
/**
* this is an implementation of an abstract Jalview GUI class that provides a
* dialog/menu which allows the user to select/deselect specific views from a
*/
package jalview.gui;
+import jalview.jbgui.GWebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.WSClientI;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
import javax.swing.text.html.HTMLEditorKit;
import javax.swing.text.html.StyleSheet;
-import jalview.jbgui.GWebserviceInfo;
-import jalview.util.MessageManager;
-import jalview.ws.WSClientI;
-
/**
* Base class for web service client thread and gui TODO: create StAX parser to
* extract html body content reliably when preparing html formatted job statuses
{
if (jobpane < 0 || jobpane >= jobPanes.size())
{
- throw new Error(MessageManager.formatMessage("error.setstatus_called_non_existent_job_pane", new String[]{Integer.valueOf(jobpane).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.setstatus_called_non_existent_job_pane",
+ new String[] { Integer.valueOf(jobpane).toString() }));
}
switch (status)
{
// anyhow - it has to stop threads and clean up
// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
// you sure?' prompt
- warnUser(MessageManager.getString("warn.job_cannot_be_cancelled_close_window"),
+ warnUser(
+ MessageManager
+ .getString("warn.job_cannot_be_cancelled_close_window"),
MessageManager.getString("action.cancel_job"));
}
else
*/
package jalview.gui;
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
+
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
/**
* job parameter editing/browsing dialog box. User can browse existing settings
* (user + presets + Defaults), and any changes to parameters creates a modified
frame = new JDialog(Desktop.instance, true);
frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
- new String[]
- { service.getActionText() }));
+ new String[] { service.getActionText() }));
Rectangle deskr = Desktop.instance.getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(new Rectangle(
WsJobParameters pgui = new WsJobParameters(lastserv,
new JabaPreset(lastserv, pr));
JFrame jf = new JFrame(MessageManager.formatMessage(
- "label.ws_parameters_for", new String[]
- { lastserv.getActionText() }));
+ "label.ws_parameters_for",
+ new String[] { lastserv.getActionText() }));
JPanel cont = new JPanel(new BorderLayout());
pgui.validate();
cont.setPreferredSize(pgui.getPreferredSize());
}
if (parser == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
}
if (filename == null)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "wsparams" }, new String[]
- { "Web Service Parameter File" },
+ { "wsparams" },
+ new String[] { "Web Service Parameter File" },
"Web Service Parameter File");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.choose_filename_for_param_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.choose_filename_for_param_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(Desktop.instance);
if (value == JalviewFileChooser.APPROVE_OPTION)
}
wsList.setModel(new WsUrlTableModel(tdat));
- wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(10);
+ wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(
+ 10);
}
private class JabaWSStatusRenderer extends JPanel implements
{
private Object[][] data;
- private String[] columnNames = new String[]
- { MessageManager.getString("label.service_url"), MessageManager.getString("label.status") };
+
+ private String[] columnNames = new String[] {
+ MessageManager.getString("label.service_url"),
+ MessageManager.getString("label.status") };
public WsUrlTableModel(Object[][] tdat)
{
@Override
public String getColumnName(int column)
{
- return columnNames[column];
+ return columnNames[column];
}
@Override
}
if (valid && resp == JOptionPane.OK_OPTION)
{
- int validate = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.getString("info.validate_jabaws_server"),
- MessageManager.getString("label.test_server"), JOptionPane.YES_NO_OPTION);
+ int validate = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString("info.validate_jabaws_server"),
+ MessageManager.getString("label.test_server"),
+ JOptionPane.YES_NO_OPTION);
if (validate == JOptionPane.OK_OPTION)
{
.getString("warn.server_didnt_pass_validation"));
}
-
}
}
else
@Override
protected void newWsUrl_actionPerformed(ActionEvent e)
{
- String url = editUrl(null, MessageManager.getString("label.add_jabaws_url"));
+ String url = editUrl(null,
+ MessageManager.getString("label.add_jabaws_url"));
if (url != null)
{
if (!wsUrls.contains(url))
public void run()
{
long ct = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_web_service_menus"),
- ct);
+ Desktop.instance.setProgressBar(MessageManager
+ .getString("status.refreshing_web_service_menus"), ct);
if (lastrefresh != update)
{
lastrefresh = update;
{
synchronized (HttpServer.class)
{
- if (instance == null) {
+ if (instance == null)
+ {
instance = new HttpServer();
}
return instance;
ch.setAllowNullPathInfo(true);
ch.setContextPath("/" + JALVIEW_PATH + "/" + path);
ch.setResourceBase(".");
- ch.setClassLoader(Thread.currentThread()
- .getContextClassLoader());
+ ch.setClassLoader(Thread.currentThread().getContextClassLoader());
ch.setHandler(handler);
/*
*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
public class AMSAFile extends jalview.io.FastaFile
{
{
this(true, inFile, type);
}
-
+
/**
- * Constructor which (optionally delays) parsing of data from a file of some specified type.
+ * Constructor which (optionally delays) parsing of data from a file of some
+ * specified type.
*
* @param parseImmediately
* if false, need to call 'doParse()' to begin parsing data
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException
+ public AlignFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
{
super(inFile, type);
initData();
- if (parseImmediately) {
+ if (parseImmediately)
+ {
doParse();
}
}
+
/**
* Attempt to read from the position where some other parsing process left
* off.
*/
public AlignFile(FileParse source) throws IOException
{
- this(true,source);
+ this(true, source);
}
+
/**
- * Construct a new parser to read from the position where some other parsing process left
+ * Construct a new parser to read from the position where some other parsing
+ * process left
*
* @param parseImmediately
* if false, need to call 'doParse()' to begin parsing data
* @param source
*/
- public AlignFile(boolean parseImmediately, FileParse source) throws IOException
+ public AlignFile(boolean parseImmediately, FileParse source)
+ throws IOException
{
super(source);
initData();
- if (parseImmediately) {
+ if (parseImmediately)
+ {
doParse();
}
}
+
/**
* called if parsing was delayed till after parser was constructed
+ *
* @throws IOException
*/
public void doParse() throws IOException
"Implementation error: Parser called twice for same data.\n"
+ "Need to call initData() again before parsing can be reattempted.");
}
- parseCalled=true;
+ parseCalled = true;
parse();
// sets the index of each sequence in the alignment
for (int i = 0, c = seqs.size(); i < c; i++)
}
}
-
/**
* Return the seqs Vector
*/
* Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
* Rna.HelixMap(pairArray);
*/
- AlignmentAnnotation an = annotations
- .elementAt(i);
+ AlignmentAnnotation an = annotations.elementAt(i);
an.validateRangeAndDisplay();
al.addAnnotation(an);
}
{
if (key == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
seqs = new Vector<SequenceI>();
annotations = new Vector<AlignmentAnnotation>();
seqGroups = new ArrayList<SequenceGroup>();
- parseCalled=false;
+ parseCalled = false;
}
/**
{
newickStrings = new Vector<String[]>();
}
- newickStrings.addElement(new String[]
- { treeName, newickString });
+ newickStrings.addElement(new String[] { treeName, newickString });
}
protected int getTreeCount()
*/
package jalview.io;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.Enumeration;
import java.util.Hashtable;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-
/**
* Render associated attributes of an alignment. The heart of this code was
* refactored from jalview.gui.AlignFrame and jalview.appletgui.AlignFrame TODO:
}
else
{
- graphGroup_refs.put(key, new Object[]
- { refSeq, refGroup });
+ graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
text.append(properties.get(key));
}
// TODO: output alignment visualization settings here if required
- // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties.
- // View specific annotation is
+ // iterate through one or more views, defining, marking columns and rows
+ // as visible/hidden, and emmitting view properties.
+ // View specific annotation is
}
return text.toString();
}
boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
file, protocol);
- if (rslt
- && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
}
return rslt;
}
+
public boolean readAnnotationFile(AlignmentI al, String file,
String protocol)
{
private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
- BufferedReader in)
- throws Exception
+ BufferedReader in) throws Exception
{
nlinesread = 0;
ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
- combineAnnotation_calls.add(new Object[]
- { st, refSeq, groupRef });
+ combineAnnotation_calls
+ .add(new Object[] { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[]
- { GRAPHLINE, st, refSeq, groupRef });
+ deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+ refSeq, groupRef });
modified = true;
continue;
}
(SequenceI) _deferred_args[2], // refSeq
(_deferred_args[3] == null) ? null : groupRefLookup
.get(_deferred_args[3]) // the reference
- // group, or null
+ // group, or null
);
}
}
(SequenceI) _combine_args[1], // refSeq
(_combine_args[2] == null) ? null : groupRefLookup
.get(_combine_args[2]) // the reference group,
- // or null
+ // or null
);
}
}
private void parseHideCols(ColumnSelection colSel, String nextToken)
{
- StringTokenizer inval = new StringTokenizer(nextToken,",");
+ StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
{
String range = inval.nextToken().trim();
/**
* List of valid format strings used in the isValidFormat method
*/
- public static final String[] READABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
- "HTML" };
+ public static final String[] READABLE_FORMATS = new String[] { "BLC",
+ "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+ "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+ IdentifyFile.GFF3File, "HTML" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
- public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ public static final String[] READABLE_EXTENSIONS = new String[] {
+ "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
"sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
- ".gff2,gff3",
- "jar,jvp", HtmlFile.FILE_EXT };
+ ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT };
/**
* List of readable formats by application in order corresponding to
* READABLE_EXTENSIONS
*/
- public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
- "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
- HtmlFile.FILE_DESC };
+ public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+ "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+ "Jalview", HtmlFile.FILE_DESC };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
- public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
- "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
+ public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
+ "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
/**
* List of extensions corresponding to file format types in WRITABLE_FNAMES
* that are writable by the application.
*/
- public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ public static final String[] WRITABLE_EXTENSIONS = new String[] {
+ "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
"sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
/**
* List of writable formats by the application. Order must correspond with the
* WRITABLE_EXTENSIONS list of formats.
*/
- public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+ public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+ "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
public static String INVALID_CHARACTERS = "Contains invalid characters";
return list.toString();
}
-
public void setNewlineString(String nl)
{
newline = nl;
}
}
-
/**
* boilerplate method to handle data from an AlignFile and construct a new
* alignment or import to an existing alignment
/**
* create an alignment flatfile from a Jalview alignment view
+ *
* @param format
* @param jvsuffix
* @param av
{
afile = new PhylipFile();
}
- else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
- {
+ else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+ {
afile = new JSONFile();
- }
+ }
else if (format.equalsIgnoreCase("RNAML"))
{
afile = new RnamlFile();
else
{
- throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
+ throw new Exception(
+ MessageManager
+ .getString("error.implementation_error_unknown_file_format_string"));
}
afile.setNewlineString(newline);
} catch (Exception e)
{
System.err
- .println("Couln't format the alignment for output as a FASTA file.");
+ .println("Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
}
System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
} catch (Exception ex)
{
System.err
- .println("Exception checking resources: " + file + " " + ex);
+ .println("Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
if (debug)
{
System.out
- .println("File deemed not accessible via " + protocol);
+ .println("File deemed not accessible via " + protocol);
}
fp.close();
return null;
}
} while (!idsFound);
if (line == null)
- {
+ {
break; // end of file.
}
int starCol = line.indexOf("*");
import java.util.Objects;
import java.util.TreeMap;
-
public class BioJsHTMLOutput
{
private AlignmentViewPanel ap;
};
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(
-JSONFile.FILE_DESC,
+ .getAlignmentForExport(JSONFile.FILE_DESC,
ap.getAlignViewport(), exportSettings);
if (exportData.getSettings().isCancelled())
{
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
+ .replaceAll("#sequenceData#", jalviewAlignmentJson)
.toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
{
String selectedFile = null;
JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "HTML files" }, "HTML files");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
jvFileChooser.setFileView(new JalviewFileView());
jvFileChooser.setDialogTitle(MessageManager
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
}
-
public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class ClustalFile extends AlignFile
{
*/
package jalview.io;
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
{
SequenceI seq = null;
/**
- * keep track of any sequences we try to create from the data if it is a GFF3 file
+ * keep track of any sequences we try to create from the data if it is a
+ * GFF3 file
*/
ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
String type, desc, token = null;
* @return true if sf was actually added to the sequence, false if it was
* processed in another way
*/
- public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ public boolean processOrAddSeqFeature(AlignmentI align,
+ List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
boolean gFFFile, boolean relaxedIdMatching)
{
String attr = (String) sf.getValue("ATTRIBUTES");
boolean add = true;
if (gFFFile && attr != null)
{
- int nattr=8;
+ int nattr = 8;
for (String attset : attr.split("\t"))
{
- if (attset==null || attset.trim().length()==0)
+ if (attset == null || attset.trim().length() == 0)
{
continue;
}
continue;
}
- // expect either space seperated (gff2) or '=' separated (gff3)
+ // expect either space seperated (gff2) or '=' separated (gff3)
// key/value pairs here
- int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+ int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
String key = null, value = null;
if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
{
key = pair.substring(0, sppos);
value = pair.substring(sppos + 1);
- } else {
+ }
+ else
+ {
if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
{
key = pair.substring(0, eqpos);
value = pair.substring(eqpos + 1);
- } else
+ }
+ else
{
key = pair;
}
{
add &= processGffKey(set, nattr, seq, sf, align, newseqs,
relaxedIdMatching); // process decides if
- // feature is actually
- // added
+ // feature is actually
+ // added
} catch (InvalidGFF3FieldException ivfe)
{
System.err.println(ivfe);
{
int strand = sf.getStrand();
// exonerate cdna/protein map
- // look for fields
+ // look for fields
List<SequenceI> querySeq = findNames(align, newseqs,
- relaxedIdMatching, set.get(attr="Query"));
- if (querySeq==null || querySeq.size()!=1)
+ relaxedIdMatching, set.get(attr = "Query"));
+ if (querySeq == null || querySeq.size() != 1)
{
- throw new InvalidGFF3FieldException( attr, set,
+ throw new InvalidGFF3FieldException(attr, set,
"Expecting exactly one sequence in Query field (got "
+ set.get(attr) + ")");
}
- if (set.containsKey(attr="Align"))
+ if (set.containsKey(attr = "Align"))
{
// process the align maps and create cdna/protein maps
// ideally, the query sequences are in the alignment, but maybe not...
-
+
AlignedCodonFrame alco = new AlignedCodonFrame();
MapList codonmapping = constructCodonMappingFromAlign(set, attr,
strand);
}
private MapList constructCodonMappingFromAlign(
- Map<String, List<String>> set,
- String attr, int strand) throws InvalidGFF3FieldException
+ Map<String, List<String>> set, String attr, int strand)
+ throws InvalidGFF3FieldException
{
if (strand == 0)
{
}
}
}
-
+
}
- if (match==null && newseqs!=null)
+ if (match == null && newseqs != null)
{
match = new SequenceDummy(seqId);
if (relaxedIdMatching)
{
- matcher.addAll(Arrays.asList(new SequenceI[]
- { match }));
+ matcher.addAll(Arrays.asList(new SequenceI[] { match }));
}
// add dummy sequence to the newseqs list
newseqs.add(match);
}
return match;
}
+
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printJalviewFormat(SequenceI[] seqs,
+ Map<String, Object> visible)
{
return printJalviewFormat(seqs, visible, true, true);
}
* @param visible
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printGFFFormat(SequenceI[] seqs, Map<String, Object> visible)
{
return printGFFFormat(seqs, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
- boolean visOnly, boolean nonpos)
+ public String printGFFFormat(SequenceI[] seqs,
+ Map<String, Object> visible, boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
}
alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new String[]
- { title }));
+ "label.successfully_loaded_file",
+ new String[] { title }));
if (raiseGUI)
{
{
javax.swing.JOptionPane.showInternalMessageDialog(
Desktop.desktop, MessageManager.formatMessage(
- "label.problems_opening_file", new String[]
- { file }), MessageManager
+ "label.problems_opening_file",
+ new String[] { file }), MessageManager
.getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
public void setNewlineString(String nl)
{
- newline = nl;
+ newline = nl;
}
public String getNewlineString()
{
if (from == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_null_fileparse"));
}
if (from == this)
{
{
if (e != null)
{
- throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+ throw new IOException(
+ MessageManager
+ .getString("exception.failed_to_resolve_gzip_stream"),
+ e);
}
throw q;
}
{
if (checkFileSource(suffixLess))
{
- throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.problem_opening_file_also_tried",
+ new String[] { inFile.getName(), suffixLess,
+ errormessage }));
}
}
else
{
- throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.problem_opening_file",
+ new String[] { inFile.getName(), errormessage }));
}
}
}
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
- {
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
}
} catch (IOException e)
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
- throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.failed_to_read_data_from_source",
+ new String[] { errormessage }));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
}
else
{
- throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+ throw new IOException(
+ MessageManager.getString("exception.no_init_source_stream"));
}
}
{
return dataIn.readLine();
}
- throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.invalid_source_stream",
+ new String[] { errormessage }));
}
/**
}
else
{
- throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
+ throw new IOException(
+ MessageManager
+ .getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
*/
public void configureForView(AlignmentViewPanel avpanel)
{
- if (avpanel!=null) {
+ if (avpanel != null)
+ {
setViewport(avpanel.getAlignViewport());
}
// could also set export/import settings
annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
- true);
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
}
else
{
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
-
if (startEnd != null)
{
startIndex = startEnd[0];
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
- suffix, colSel,
- null);
+ suffix, colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
- ColumnSelection colSel,
- jalview.datamodel.SequenceGroup selgp)
+ ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
{
if (omitHidden != null)
{
selectedOnly);
}
-
}
AlignmentI dataset;
List<AlignmentI> alignments;
+
@Override
public void parse()
{
}
else
{
- dataset = new Alignment(new SequenceI[]
- {});
+ dataset = new Alignment(new SequenceI[] {});
}
boolean parseResult = parse(dataset, null, null, false, true);
*/
package jalview.io;
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Font;
+import java.io.PrintWriter;
+
public class HTMLOutput
{
AlignViewport av;
fr.transferSettings(fr1);
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "HTML files" }, "HTML files");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
throw new IOException(errormessage);
}
JSONFile jsonFile = new JSONFile().parse(new StringReader(
- contentFromDiv ? content.text() : content
- .val()));
+ contentFromDiv ? content.text() : content.val()));
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
}
}
-
@Override
public String print()
{
AlignViewport av;
FeatureRenderer fr;
- AlignmentPanel ap;
+ AlignmentPanel ap;
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
if (file == null)
{
- JalviewFileChooser chooser = getHTMLChooser();
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(ap.alignFrame.getTitle());
- chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(ap.alignFrame);
+ JalviewFileChooser chooser = getHTMLChooser();
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle(ap.alignFrame.getTitle());
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+ int value = chooser.showSaveDialog(ap.alignFrame);
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
- file = chooser.getSelectedFile();
- }
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
+ file = chooser.getSelectedFile();
+ }
}
AlignmentDimension aDimension = ap.getAlignmentDimension();
.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
if (isEmbbedBioJSON)
{
- AlignExportSettingI exportSettings = new AlignExportSettingI(){
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
@Override
public boolean isExportHiddenSequences()
{
{
return false;
}
-
+
};
AlignmentExportData exportData = jalview.gui.AlignFrame
.getAlignmentForExport(JSONFile.FILE_DESC, av,
exportSettings);
jsonData = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC, exportData
- .getAlignment(), exportData.getOmitHidden(),
+ .formatSequences(JSONFile.FILE_DESC,
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
exportData.getStartEndPostions(),
av.getColumnSelection());
}
if (!(System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true")))
{
- jalview.util.BrowserLauncher.openURL("file:///" + file);
+ jalview.util.BrowserLauncher.openURL("file:///" + file);
}
} catch (Exception e)
{
e.printStackTrace();
}
}
-
+
static JalviewFileChooser getHTMLChooser()
{
return new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "Hypertext Markup Language" }, "Hypertext Markup Language");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" },
+ new String[] { "Hypertext Markup Language" },
+ "Hypertext Markup Language");
}
public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
- fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
- 4;
}
- pg[0].drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
+ pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
return Printable.PAGE_EXISTS;
}
-
+
private String getHtml(String titleSvg, String alignmentSvg,
String jsonData)
{
htmlSvg.append("<div class=\"align\" >");
htmlSvg.append(
"<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
- .append(alignmentSvg)
-.append("</div></div>")
- .append("</div>");
+ .append(alignmentSvg).append("</div></div>").append("</div>");
htmlSvg.append("</div>");
htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
break;
}
-
/*
* // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
* if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
* "SimpleBLAST"; break;
- *
+ *
* } // end comments for Jalview 2.4.1
*/
else if (!lineswereskipped && data.charAt(0) != '*'
&& data.charAt(0) != ' '
&& data.indexOf(":") < data.indexOf(",")) // &&
- // data.indexOf(",")<data.indexOf(",",
- // data.indexOf(",")))
+ // data.indexOf(",")<data.indexOf(",",
+ // data.indexOf(",")))
{
// file looks like a concise JNet file
reply = "JnetFile";
if (length == 0)
{
System.err
- .println("File Identification failed! - Empty file was read.");
+ .println("File Identification failed! - Empty file was read.");
return "EMPTY DATA FILE";
}
return reply;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
/**
* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
* line is either a sequence (QUERY), a sequence profile (align;), or jnet
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()}));
+ throw new IOException(
+ MessageManager
+ .formatMessage(
+ "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+ new String[] { ids.elementAt(i).toString() }));
}
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()}));
+ IOException ex = new IOException(
+ MessageManager
+ .formatMessage(
+ "exception.couldnt_parse_concise_annotation_for_prediction",
+ new String[] { e.getMessage() }));
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
&& getSelectedFile().exists())
{
int confirm = JOptionPane.showConfirmDialog(parent,
- MessageManager.getString("label.overwrite_existing_file"), MessageManager.getString("label.file_already_exists"),
+ MessageManager.getString("label.overwrite_existing_file"),
+ MessageManager.getString("label.file_already_exists"),
JOptionPane.YES_NO_OPTION);
if (confirm != JOptionPane.YES_OPTION)
}
});
- this.setBorder(new javax.swing.border.TitledBorder(MessageManager.getString("label.recently_opened")));
+ this.setBorder(new javax.swing.border.TitledBorder(MessageManager
+ .getString("label.recently_opened")));
final JScrollPane scroller = new JScrollPane(list);
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import java.io.File;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
import javax.swing.filechooser.FileFilter;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import java.io.File;
+import java.util.Hashtable;
-import javax.swing.*;
-import javax.swing.filechooser.*;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.filechooser.FileView;
public class JalviewFileView extends FileView
{
MessageManager
.formatMessage(
"exception.number_of_residues_in_query_sequence_differ_from_prediction",
- new String[]
- {
+ new String[] {
(delMap == null ? "" : MessageManager
.getString("label.mapped")),
al.getSequenceAt(firstSeq).getName(),
*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
public class ModellerDescription
{
* single line, and sequence start/end and other properties. See PIRFile IO
* for its use.
*/
- final String[] seqTypes =
- { "sequence", "structure", "structureX", "structureN" };
+ final String[] seqTypes = { "sequence", "structure", "structureX",
+ "structureN" };
- final String[] Fields =
- { "objectType", "objectId", "startField", "startCode", "endField",
- "endCode", "description1", "description2", "resolutionField",
- "tailField" };
+ final String[] Fields = { "objectType", "objectId", "startField",
+ "startCode", "endField", "endCode", "description1", "description2",
+ "resolutionField", "tailField" };
final int TYPE = 0;
/**
* 0 is free text or empty 1 is something that parses to an integer, or \@
*/
- final int Types[] =
- { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+ final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
- final char Padding[] =
- { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+ final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
java.util.Hashtable fields = new java.util.Hashtable();
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.io.*;
-import java.util.StringTokenizer;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
+
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
if (Error != null)
{
- throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()})));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { Error.toString() })));
}
if (root == null)
{
- throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{MessageManager.getString("label.no_tree_read_in")})));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { MessageManager
+ .getString("label.no_tree_read_in") })));
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
public class PIRFile extends AlignFile
{
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class PfamFile extends AlignFile
{
if (noSeqs < 1)
{
- throw new IOException(MessageManager.getString("exception.pfam_no_sequences_found"));
+ throw new IOException(
+ MessageManager.getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
*/
private String validateName(String name) throws IOException
{
- char[] invalidCharacters = new char[]
- { '(', ')', '[', ']', ':', ';', ',' };
+ char[] invalidCharacters = new char[] { '(', ')', '[', ']', ':', ';',
+ ',' };
for (char c : invalidCharacters)
{
if (name.indexOf(c) > -1)
* found in Emboss (thanks David Martin!)
*
*/
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
public class PileUpfile extends MSFfile
{
_parse();
} catch (ExceptionPermissionDenied pdx)
{
- errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.rnaml_couldnt_access_datasource",
+ new String[] { pdx.getMessage() });
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
- errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_couldnt_process_data",
+ new String[] { lf.getMessage() });
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_invalid_file",
+ new String[] { iff.getMessage() });
throw new IOException(iff);
} catch (Exception x)
{
error = true;
- errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
- throw new IOException(errormessage , x);
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_problem_parsing_data",
+ new String[] { x.getMessage() });
+ throw new IOException(errormessage, x);
}
}
*/
package jalview.io;
-
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
import java.util.List;
-
/**
* generate HTML reports for a sequence
*
String tmpString;
if (features != null)
{
- for (SequenceFeature feature:features)
+ for (SequenceFeature feature : features)
{
if (feature.getType().equals("disulfide bond"))
{
- if (feature.getBegin() == rpos
- || feature.getEnd() == rpos)
+ if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
if (tooltipText2.length() > 6)
{
}
if (feature.getDescription() != null
- && !feature.description.equals(feature
- .getType()))
+ && !feature.description.equals(feature.getType()))
{
tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
- new String[]
- { target });
+ new String[] { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- urlSets.add(new String[]
- { target, label, urls[u], urls[u + 1] });
+ urlSets.add(new String[] { target, label, urls[u],
+ urls[u + 1] });
uniques.add(unq);
}
}
{
uniques.add(unq);
// Add a non-dynamic link
- urlSets.add(new String[]
- { target, label, null, urlLink.getUrl_prefix() });
+ urlSets.add(new String[] { target, label, null,
+ urlLink.getUrl_prefix() });
}
}
- return urlSets.toArray(new String[][]
- {});
+ return urlSets.toArray(new String[][] {});
}
public void createSequenceAnnotationReport(final StringBuffer tip,
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* parse a simple blast report. Attempt to cope with query anchored and pairwise
if (seqentry == null)
{
padseq = true; // prepend gaps to new sequences in this block
- seqentry = new Object[]
- { new StringBuffer(), new long[]
- { rstart, rend } };
+ seqentry = new Object[] { new StringBuffer(),
+ new long[] { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
{
// logger.error("Could not parse sequence line: " + line);
throw new IOException(MessageManager.formatMessage(
- "exception.couldnt_parse_sequence_line", new String[]
- { line }));
+ "exception.couldnt_parse_sequence_line",
+ new String[] { line }));
}
String ns = seqs.get(x.stringMatched(1));
if (ns == null)
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unknown_annotation_detected", new String[]
- { annType, annContent }));
+ "exception.unknown_annotation_detected", new String[] {
+ annType, annContent }));
}
}
}
{
for (DBRefEntry d : dbrs)
{
- jalview.util.MapList mp = new jalview.util.MapList(new int[]
- { seqO.getStart(), seqO.getEnd() }, new int[]
- { st, en }, 1, 1);
+ jalview.util.MapList mp = new jalview.util.MapList(new int[] {
+ seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
jalview.datamodel.Mapping mping = new Mapping(mp);
d.setMap(mping);
}
// be written out
if (ss)
{
- //if (" .-_".indexOf(pos) == -1)
+ // if (" .-_".indexOf(pos) == -1)
{
if (detectbrackets.search(pos))
{
ann.displayCharacter = " " + ann.displayCharacter;
}
}
-
+
}
els[i] = ann;
* @param ann
* @param sequenceI
*/
- private char outputCharacter(String key, int k,
- boolean isrna, Annotation[] ann, SequenceI sequenceI)
+ private char outputCharacter(String key, int k, boolean isrna,
+ Annotation[] ann, SequenceI sequenceI)
{
char seq = ' ';
Annotation annot = ann[k];
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
- .toString(sequenceI.getCharAt(k)))
- : annot.displayCharacter;
+ .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
if (key != null && key.equals("SS"))
{
if (annot == null)
{
// sensible gap character if one is available or make one up
- return sequenceI == null ? '-' : sequenceI
- .getCharAt(k);
+ return sequenceI == null ? '-' : sequenceI.getCharAt(k);
}
else
{
/**
* TCOFFEE score colourscheme
*/
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
- "Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
end = start;
start = t;
}
- return new int[]
- { start, end, pol < 0 ? 1 : 0 };
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
/**
{
// NOTE: this happens if user deletes object in one session then updates
// from another client
- throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[] { oldjvobject.toString() }));
}
if (newjvobject != null)
{
// may not quite cope with this (without binding an array of annotations to
// a vamsas alignment annotation)
// summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[]
- { false, false, false, false, false };
+ boolean[] AeContent = new boolean[] { false, false, false, false, false };
int[] rangeMap = getMapping(annotation);
jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
{ new jalview.datamodel.Annotation[rangeMap.length],
anot[1][i].description = anot[1][i].description + " (after)";
}
}
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
else
{
// no annotations to parse. Just return an empty annotationElement[]
// array.
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
// return null;
}
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
- se = new int[]
- { pos, pos };
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
}
} catch (Exception e)
{
- throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
+ throw new Exception(MessageManager.formatMessage(
+ "exception.couldnt_store_sequence_mappings",
+ new String[] { title }), e);
}
}
*/
package jalview.io;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import uk.ac.ebi.www.*;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
/**
* DOCUMENT ME!
{
maxFound = value;
buffer.append(" " + id2 + " " + value + "%; ");
- suggestedIds.addElement(new Object[]
- { seq, id2 });
+ suggestedIds.addElement(new Object[] { seq, id2 });
}
}
}
imageIndex++;
imageIndex %= 9;
output.setFrameIcon(imageIcon[imageIndex]);
- output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{Integer.valueOf(jobsRunning).toString()}));
+ output.setTitle(MessageManager.formatMessage(
+ "label.blasting_for_unidentified_sequence_jobs_running",
+ new String[] { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
+
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Sequence;
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
- "Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
- "Warning? Overwriting existing jalview object binding for "
- + jvobj, new Exception(MessageManager.getString("exception.overwriting_jalview_id_binding")));
+ Cache.log
+ .debug("Warning? Overwriting existing jalview object binding for "
+ + jvobj,
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_jalview_id_binding")));
}
/*
* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[] { oldjvobject.toString() }));
}
if (newjvobject != null)
{
tojalview = true;
if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
- , new String[]{vobj.getClass().toString(),boundType.toString(),jvobj.getClass().toString()}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+ new String[] { vobj.getClass().toString(),
+ boundType.toString(),
+ jvobj.getClass().toString() }));
}
dsReg.registerDsObj(this);
}
vobj = getjv2vObj(jvobj);
if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
- , new String[]{jvobj2.getClass().toString(),boundToType.toString(),vobj.getClass().toString()}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+ new String[] { jvobj2.getClass().toString(),
+ boundToType.toString(),
+ vobj.getClass().toString() }));
}
dsReg.registerDsObj(this);
}
end = start;
start = t;
}
- return new int[]
- { start, end, pol < 0 ? 1 : 0 };
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
/**
if (dsregitem == null)
{
// create a new item entry
- dsregitem = new Object[]
- { dsitem.jvobj, dsitem.vobj };
+ dsregitem = new Object[] { dsitem.jvobj, dsitem.vobj };
dsItemReg.put(dsitem, dsregitem);
dsObjReg.put(dsitem.jvobj, dsitem);
dsObjReg.put(dsitem.vobj, dsitem);
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Map;
import uk.ac.vamsas.objects.core.Sequence;
-import jalview.io.VamsasAppDatastore;
public class Dbref extends Rangetype
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
- se = new int[]
- { pos, pos };
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
{
if (ml == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
.debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
- dsa.setSeg(new Seg[]
- { vSeg });
+ dsa.setSeg(new Seg[] { vSeg });
dsa.setDescription(feature.getDescription());
dsa.setStatus(feature.getStatus());
if (feature.links != null && feature.links.size() > 0)
if (!Float.isNaN(feature.getScore()))
{
Score fscore = new Score();
- dsa.setScore(new Score[]
- { fscore });
+ dsa.setScore(new Score[] { fscore });
fscore.setContent(feature.getScore());
fscore.setName(feature.getType());
}
}
bindjvvobj(mapping, sequenceMapping);
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).registerMapping(acf);
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
// Try to propagate any dbrefs across this mapping.
*/
package jalview.io.vamsas;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.NJTree;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
tnv.copyInto(tn);
return tn;
}
- return new Treenode[]
- {};
+ return new Treenode[] {};
}
private String makeNodeSpec(Hashtable nodespecs,
// off by
// one for to
}
- return new Object[]
- { new AlignmentView(view), jal };
+ return new Object[] { new AlignmentView(view), jal };
}
}
Cache.log
*/
package jalview.javascript;
+import jalview.bin.JalviewLite;
+
import java.net.URL;
import java.util.Vector;
import netscape.javascript.JSObject;
-import jalview.bin.JalviewLite;
public class JSFunctionExec implements Runnable
{
}
}
- String[] seqs = new String[]
- {};
- String[] cols = new String[]
- {};
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
int strt = 0, end = (src == null) ? -1 : src.alignPanel.av
.getAlignment().getWidth();
if (seqsel != null && seqsel.getSize() > 0)
}
System.err.println("Relaying selection to jsfunction:" + _listener);
- executeJavascriptFunction(
- _listener,
- new Object[]
- { src, setid, jvlite.arrayToSeparatorList(seqs),
+ executeJavascriptFunction(_listener,
+ new Object[] { src, setid, jvlite.arrayToSeparatorList(seqs),
jvlite.arrayToSeparatorList(cols) });
} catch (Exception ex)
{
// function, then only events from that alignFrame are sent to that
// function
}
- executeJavascriptFunction(
- _listener,
- new Object[]
- { src, seq.getDisplayId(false), "" + (1 + i),
+ executeJavascriptFunction(_listener,
+ new Object[] { src, seq.getDisplayId(false), "" + (1 + i),
"" + seq.findPosition(i) });
} catch (Exception ex)
{
// field that is interpreted (in 2.8.2) as pdbId?
// JBPComment: yep - this is right! the Javascript harness uses the
// absolute pdbFile URI to locate the PDB file in the external viewer
- executeJavascriptFunction(_listenerfn, new String[]
- { "mouseover", "" + atom.getPdbFile(),
- "" + atom.getChain(),
- "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
+ executeJavascriptFunction(_listenerfn,
+ new String[] { "mouseover", "" + atom.getPdbFile(),
+ "" + atom.getChain(), "" + (atom.getPdbResNum()),
+ "" + atom.getAtomIndex() });
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
{
jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
// and notify javascript handler
- String st[] = new String[]
- {
+ String st[] = new String[] {
"colourstruct",
"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
"" + ccomandset.length,
{
this.hasHiddenSeq = hasHiddenSeq;
this.hasHiddenCols = hasHiddenCols;
- String[] complexFormats =
- { "JSON", "HTML" };
+ String[] complexFormats = { "JSON", "HTML" };
for (String format : complexFormats)
{
add(actionPanel, BorderLayout.SOUTH);
}
-
+
private void checkAllAction()
{
boolean isSelected = chkAll.isSelected();
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
- MessageManager
- .getString("action.select_all"));
+ MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
}
});
- JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-.getString("action.remove_redundancy"));
+ JMenuItem removeRedundancyMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.ALT_MASK, false);
al = new ActionListener()
{
{
}
+
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
return annotationSortOrder;
}
- protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
{
this.annotationSortOrder = annotationSortOrder;
}
*/
package jalview.jbgui;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.border.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JPanel;
+import javax.swing.JScrollBar;
+import javax.swing.JScrollPane;
+import javax.swing.border.Border;
public class GAlignmentPanel extends JPanel
{
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
/**
* DOCUMENT ME!
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
/**
* DOCUMENT ME!
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
public class GDasSourceBrowser extends JPanel
{
JMenuItem saveState = new JMenuItem();
JMenuItem loadState = new JMenuItem();
-
+
JMenu inputMenu = new JMenu();
protected JMenuItem vamsasStart = new JMenuItem();
protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
-
+
protected JMenuItem snapShotWindow = new JMenuItem();
+
/**
* Creates a new GDesktop object.
*/
snapShotWindow_actionPerformed(e);
}
});
-
+
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
VamsasMenu.setVisible(false);
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showConsole_actionPerformed(ActionEvent e)
}
}
-
private void jbInit() throws Exception
{
jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
*/
package jalview.jbgui;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.JPanel;
import javax.swing.SwingConstants;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-
/**
* DOCUMENT ME!
*
*/
public class GFontChooser extends JPanel
{
- private static final Font VERDANA_11PT = new java.awt.Font("Verdana", 0, 11);
+ private static final Font VERDANA_11PT = new java.awt.Font("Verdana", 0,
+ 11);
protected JComboBox<Integer> fontSize = new JComboBox<Integer>();
protected JButton btn_ok = new JButton();
protected JButton btn_back = new JButton();
-
+
protected JButton btn_cancel = new JButton();
-
+
protected JTextField txt_search = new JTextField(20);
-
+
protected JTable tbl_summary = new JTable()
{
public String getToolTipText(MouseEvent evt)
}
toolTipText = (toolTipText == null ? null
: (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
- true, toolTipText.subSequence(0, 500)
- + "...")
- : JvSwingUtils.wrapTooltip(true,
- toolTipText)));
+ true, toolTipText.subSequence(0, 500) + "...")
+ : JvSwingUtils.wrapTooltip(true, toolTipText)));
return toolTipText;
}
protected StringBuilder errorWarning = new StringBuilder();
- protected JScrollPane scrl_searchResult = new JScrollPane(
-tbl_summary);
+ protected JScrollPane scrl_searchResult = new JScrollPane(tbl_summary);
protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
"/images/warning.gif"));
protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
"/images/loading.gif"));
+
protected JLabel lbl_warning = new JLabel(warningImage);
protected JLabel lbl_loading = new JLabel(loadingImage);
{
validateSelection();
}
+
public void mouseReleased(MouseEvent e)
{
validateSelection();
}
});
-
scrl_searchResult.setPreferredSize(new Dimension(500, 300));
scrl_searchResult
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
else
{
tooltipText = MessageManager.formatMessage(
- "label.separate_multiple_query_values", new Object[]
- { getCmbSearchTarget().getSelectedItem().toString() });
+ "label.separate_multiple_query_values",
+ new Object[] { getCmbSearchTarget().getSelectedItem()
+ .toString() });
}
txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
tooltipText));
populateCmbSearchTargetOptions();
-
txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
txt_search.addKeyListener(new KeyAdapter()
final String searchTabTitle = MessageManager
.getString("label.search_result");
- final String configureCols = MessageManager.getString("label.configure_displayed_columns");
+ final String configureCols = MessageManager
+ .getString("label.configure_displayed_columns");
ChangeListener changeListener = new ChangeListener()
{
public void stateChanged(ChangeEvent changeEvent)
: true;
}
+
public void validateSelection()
{
if (tbl_summary.getSelectedRows().length > 0)
btn_ok.setEnabled(false);
}
}
+
public JComboBox<PDBDocField> getCmbSearchTarget()
{
return cmb_searchTarget;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
/**
* DOCUMENT ME!
{
private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- private static final Font LABEL_FONT_ITALIC = JvSwingUtils
- .getLabelFont(false, true);
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+ false, true);
/*
* Visual tab components
protected JTextField chimeraPath = new JTextField();
-
/*
* Colours tab components
*/
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
- tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
/*
* See DasSourceBrowser for the real work of configuring this tab.
*/
dasTab.setLayout(new BorderLayout());
- tabbedPane
- .add(dasTab, MessageManager.getString("label.das_settings"));
+ tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
/*
* See WsPreferences for the real work of configuring this tab.
autoIdWidth.setFont(LABEL_FONT);
autoIdWidth.setText(MessageManager
.getString("label.automatically_set_id_width"));
- autoIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
autoIdWidth.addActionListener(new ActionListener()
{
userIdWidthlabel.setText(MessageManager
.getString("label.figure_id_column_width"));
userIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
userIdWidthlabel
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
nucColourLabel.setFont(LABEL_FONT);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(MessageManager
- .getString("label.nuc_alignment_colour")
- + " ");
+ .getString("label.nuc_alignment_colour") + " ");
JvSwingUtils.addtoLayout(coloursTab, MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
int ypos = 30;
structFromPdb.setFont(LABEL_FONT);
- structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
structFromPdb.addActionListener(new ActionListener()
{
docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
structureTab.add(docFieldPref);
-
-
-
return structureTab;
}
-
/**
* Action on choosing a structure viewer from combobox options.
*
}
}
});
-
+
sortby.setFont(LABEL_FONT);
sortby.setBounds(new Rectangle(172, 260, 155, 21));
JLabel sortLabel = new JLabel();
*/
package jalview.jbgui;
-import java.awt.Dimension;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
import jalview.gui.JvSwingUtils;
import jalview.gui.OptsAndParamsPage;
import jalview.util.MessageManager;
-import javax.swing.*;
+import java.awt.Dimension;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
import javax.swing.border.TitledBorder;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
// details.add(cpanel = new JPanel(), BorderLayout.CENTER);
// cpanel.setLayout(new FlowLayout());
hSeparable = new JCheckBox(MessageManager.getString("label.per_seq"));
- hSeparable
- .setToolTipText(JvSwingUtils
- .wrapTooltip(true, MessageManager.getString("label.job_created_when_checked")));
+ hSeparable.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.job_created_when_checked")));
hSeparable.addActionListener(new ActionListener()
{
vSeparable = new JCheckBox(
MessageManager.getString("label.result_vertically_separable"));
vSeparable
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.when_checked_job_visible_region_and_results")));
+ .setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ MessageManager
+ .getString("label.when_checked_job_visible_region_and_results")));
vSeparable.addActionListener(new ActionListener()
{
.getString("label.rsbs_encoded_service")));
urldescPane.add(urldescVp, "span");
paste.add(urldescPane, "span");
- urldescPane
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.flat_file_representation")));
+ urldescPane.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.flat_file_representation")));
parseRes = new JTextArea();
parseResVp = new JScrollPane();
"[grow 100, fill]"));
parseWarnings.setBorder(new TitledBorder(MessageManager
.getString("label.parsing_errors")));
- parseWarnings
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.result_of_parsing_rsbs")));
+ parseWarnings.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.result_of_parsing_rsbs")));
parseWarnings.add(parseResVp, "center");
parseRes.setEditable(false);
paste.add(parseWarnings, "span");
*/
package jalview.jbgui;
-import javax.swing.*;
+import javax.swing.JInternalFrame;
public class GRnaStructureViewer extends JInternalFrame
{
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
public class GSequenceLink extends Panel
{
return true;
}
- JOptionPane
- .showInternalMessageDialog(
- jalview.gui.Desktop.desktop,
- MessageManager.getString("warn.url_must_contain"),
- MessageManager.getString("label.invalid_url"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+ MessageManager.getString("warn.url_must_contain"),
+ MessageManager.getString("label.invalid_url"),
+ JOptionPane.WARNING_MESSAGE);
return false;
}
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
/**
* DOCUMENT ME!
package jalview.jbgui;
+import jalview.util.Platform;
+
import java.awt.Component;
import java.awt.MouseInfo;
import java.awt.Point;
import javax.swing.JSplitPane;
import javax.swing.plaf.basic.BasicInternalFrameUI;
-import jalview.util.Platform;
-
public class GSplitFrame extends JInternalFrame
{
private static final long serialVersionUID = 1L;
protected GAlignFrame getFrameAtMouse()
{
Point loc = MouseInfo.getPointerInfo().getLocation();
-
+
if (isIn(loc, splitPane.getTopComponent()))
{
return getTopFrame();
protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
protected AlignmentPanel ap;
-
+
protected StringBuilder errorWarning = new StringBuilder();
protected JLabel lbl_result = new JLabel(
protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
-
protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
}
};
- protected JScrollPane scrl_foundStructures = new JScrollPane(
- tbl_summary);
+ protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
protected JTable tbl_local_pdb = new JTable();
PreferenceSource.STRUCTURE_CHOOSER);
protected PDBDocField[] previousWantedFields;
+
public GStructureChooser()
{
try
pnl_main.add(chk_invertFilter);
lbl_loading.setVisible(false);
-
pnl_fileChooser.add(btn_pdbFromFile);
pnl_fileChooser.add(lbl_fromFileStatus);
pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
pnl_idInput.add(lbl_pdbManualFetchStatus);
pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
-
+
final String foundStructureSummary = MessageManager
.getString("label.found_structures_summary");
final String configureCols = MessageManager
JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
.getSource();
int index = sourceTabbedPane.getSelectedIndex();
- if (sourceTabbedPane.getTitleAt(index)
-.equals(configureCols))
+ if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
{
btn_view.setEnabled(false);
btn_cancel.setEnabled(false);
pnl_filter.setPreferredSize(new Dimension(500, 300));
pnl_filter.add(foundStructureSummary, scrl_foundStructures);
pnl_filter.add(configureCols, pdbDocFieldPrefs);
-
+
pnl_locPDB.add(scrl_localPDB);
pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
-
+
this.setLayout(mainLayout);
this.add(pnl_main, java.awt.BorderLayout.NORTH);
this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
previousWantedFields) ? false : true;
}
-
+
@Override
/**
* Event listener for the 'filter' combo-box and 'invert' check-box
public class AssociateSeqOptions
{
private SequenceI sequence;
+
private String name;
public AssociateSeqOptions(SequenceI seq)
*/
package jalview.jbgui;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.util.MessageManager;
+
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.util.MessageManager;
-
public abstract class GStructureViewer extends JInternalFrame implements
JalviewStructureDisplayI
{
colourMenu.setText(MessageManager.getString("label.colours"));
JMenuItem backGround = new JMenuItem();
- backGround.setText(MessageManager.getString("action.background_colour"));
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
backGround.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
import javax.swing.colorchooser.AbstractColorChooserPanel;
/**
label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
label.setOpaque(false);
label.setPreferredSize(new Dimension(260, 34));
- label.setText(MessageManager.formatMessage(
- "label.html_content",
- new String[]
- { MessageManager
- .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
+ label.setText(MessageManager
+ .formatMessage(
+ "label.html_content",
+ new String[] { MessageManager
+ .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
this.add(jPanel4, java.awt.BorderLayout.CENTER);
this.add(colorChooser, java.awt.BorderLayout.EAST);
-
+
AbstractColorChooserPanel[] choosers = colorChooser.getChooserPanels();
- // JAL-1360 larger JColorChooser in Java 7 overwrites AA panel; restrict to swatch picker only
- if (choosers.length > 3) {
- // Java 7 default has 5 options rather than 3 for choosing colours; keep the first only
- colorChooser.setChooserPanels(new AbstractColorChooserPanel[]{choosers[0]});
+ // JAL-1360 larger JColorChooser in Java 7 overwrites AA panel; restrict to
+ // swatch picker only
+ if (choosers.length > 3)
+ {
+ // Java 7 default has 5 options rather than 3 for choosing colours; keep
+ // the first only
+ colorChooser
+ .setChooserPanels(new AbstractColorChooserPanel[] { choosers[0] });
}
}
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
/**
* DOCUMENT ME!
switch (source)
{
case SEARCH_SUMMARY:
- columnNames = new String[]
- { "PDB Field", "Show in search summary" };
+ columnNames = new String[] { "PDB Field", "Show in search summary" };
break;
case STRUCTURE_CHOOSER:
- columnNames = new String[]
- { "PDB Field", "Show in structure summary" };
+ columnNames = new String[] { "PDB Field", "Show in structure summary" };
break;
case PREFERENCES:
- columnNames = new String[]
- { "PDB Field", "Show in search summary", "Show in structure summary" };
+ columnNames = new String[] { "PDB Field", "Show in search summary",
+ "Show in structure summary" };
break;
default:
break;
switch (source)
{
case SEARCH_SUMMARY:
- data[x++] = new Object[]
- { field.getName(), searchSummaryFields.contains(field) };
+ data[x++] = new Object[] { field.getName(),
+ searchSummaryFields.contains(field) };
break;
case STRUCTURE_CHOOSER:
- data[x++] = new Object[]
- { field.getName(), structureSummaryFields.contains(field) };
+ data[x++] = new Object[] { field.getName(),
+ structureSummaryFields.contains(field) };
break;
case PREFERENCES:
- data[x++] = new Object[]
- { field.getName(), searchSummaryFields.contains(field),
+ data[x++] = new Object[] { field.getName(),
+ searchSummaryFields.contains(field),
structureSummaryFields.contains(field) };
break;
default:
}
private void updatePrefs(Collection<PDBDocField> prefConfig,
- PDBDocField pdbField,
- boolean selected)
+ PDBDocField pdbField, boolean selected)
{
if (prefConfig.contains(pdbField) && !selected)
{
this.latestReleaseVersion = (String) JsonObj
.get("latestReleaseVersion");
- JSONArray repositoriesJsonArray = (JSONArray) JsonObj
-.get("releases");
+ JSONArray repositoriesJsonArray = (JSONArray) JsonObj.get("releases");
for (Iterator<JSONObject> repoIter = repositoriesJsonArray.iterator(); repoIter
.hasNext();)
{
this.description = description;
}
-
public String getLatestReleaseVersion()
{
return latestReleaseVersion;
public class AlignmentAnnotationPojo
{
- @Attributes(required = false, description = "Label for the Alignment Annotation")
+ @Attributes(
+ required = false,
+ description = "Label for the Alignment Annotation")
private String label;
- @Attributes(required = false, description = "Description for the Alignment Annotation")
+ @Attributes(
+ required = false,
+ description = "Description for the Alignment Annotation")
private String description;
@Attributes(required = false)
this.annotations = annotations;
}
-
-
}
package jalview.json.binding.biojson.v1;
-
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import com.github.reinert.jjschema.Attributes;
-@Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
+@Attributes(
+ title = "BioJSON",
+ description = "A specification for the representation and exchange of bioinformatics data")
public class AlignmentPojo
{
- @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
+ @Attributes(
+ required = true,
+ description = "Serial version identifier for <b>BioJSON</b> schema")
private String svid = "1.0";
@Attributes(
required = true,
minItems = 1,
- description = "An array of Sequences which makes up the Alignment")
+ description = "An array of Sequences which makes up the Alignment")
private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
@Attributes(
"Blosum62", "RNA Helices", "% Identity" },
description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the alignment")
private String colourScheme;
-
+
@Attributes(
- required = true,
- maxItems = 0, description = "AppSettings stores key=value pairs of custom application specific <br>"
- + "settings (i.e visualisation settings, etc) for different applications<br>"
- + "that consume or generate BioJSON")
+ required = true,
+ maxItems = 0,
+ description = "AppSettings stores key=value pairs of custom application specific <br>"
+ + "settings (i.e visualisation settings, etc) for different applications<br>"
+ + "that consume or generate BioJSON")
Map<String, Object> appSettings = new HashMap<String, Object>();
public AlignmentPojo()
public class AnnotationPojo
{
- @Attributes(required = false, description = "Display character for the given annotation")
+ @Attributes(
+ required = false,
+ description = "Display character for the given annotation")
private String displayCharacter;
- @Attributes(required = false, description = "Description for the annotation")
+ @Attributes(
+ required = false,
+ description = "Description for the annotation")
private String description;
- @Attributes(required = true, enums = {"E", "H", "\u0000", ")", "("}, description = "Determines what is rendered for the secondary </br>structure <ul><li>’E’ - indicates Beta Sheet/Strand <li>’H’ - indicates alpha helix </li><li> ‘\\u0000’ - indicates blank</li></ul></br>For RNA Helix (only shown when working with</br> nucleotide sequences): <ul><li> ‘(’ - indicates bases pair with columns upstream</br> (to right) </li><li> ’(’ - indicate region pairs with bases to the left</li></ul>")
+ @Attributes(
+ required = true,
+ enums = { "E", "H", "\u0000", ")", "(" },
+ description = "Determines what is rendered for the secondary </br>structure <ul><li>’E’ - indicates Beta Sheet/Strand <li>’H’ - indicates alpha helix </li><li> ‘\\u0000’ - indicates blank</li></ul></br>For RNA Helix (only shown when working with</br> nucleotide sequences): <ul><li> ‘(’ - indicates bases pair with columns upstream</br> (to right) </li><li> ’(’ - indicate region pairs with bases to the left</li></ul>")
private char secondaryStructure;
@Attributes(required = false, description = "Value of the annotation")
private float value;
-
public String getDisplayCharacter()
{
return displayCharacter;
public class SequenceFeaturesPojo
{
- @Attributes(required = true, description = "Start residue position for the sequence feature")
+ @Attributes(
+ required = true,
+ description = "Start residue position for the sequence feature")
private int xStart;
- @Attributes(required = true, description = "End residue position for the sequence feature")
+ @Attributes(
+ required = true,
+ description = "End residue position for the sequence feature")
private int xEnd;
@Attributes(
description = "Reference to the sequence in the alignment<br> (more like a foreign key)")
private String sequenceRef;
- @Attributes(required = true, description = "The name or type of the SequenceFeature")
+ @Attributes(
+ required = true,
+ description = "The name or type of the SequenceFeature")
private String type;
@Attributes(required = false, description = "Score")
@Attributes(required = false, description = "Description for the feature")
private String description;
-
- @Attributes(required = false, description = "Additional metadata for the feature")
+
+ @Attributes(
+ required = false,
+ description = "Additional metadata for the feature")
private Map<String, Object> otherDetails;
@Attributes(required = false, description = "Fill colour")
@Attributes(required = true, description = "Feature group")
private String featureGroup;
- @Attributes(required = false, description = "URL links associated to the feature")
+ @Attributes(
+ required = false,
+ description = "URL links associated to the feature")
private Vector<String> links;
public SequenceFeaturesPojo()
description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group")
private String colourScheme;
- @Attributes(required = true, description = "The name assigned to the seqGroup")
+ @Attributes(
+ required = true,
+ description = "The name assigned to the seqGroup")
private String groupName;
- @Attributes(required = false, description = "Serial version identifier for the <b>seqGroup</b> object model")
+ @Attributes(
+ required = false,
+ description = "Serial version identifier for the <b>seqGroup</b> object model")
private String description;
- @Attributes(required = false, description = "Determines if the seqGroup border should be visible or not")
+ @Attributes(
+ required = false,
+ description = "Determines if the seqGroup border should be visible or not")
private boolean displayBoxes;
- @Attributes(required = false, description = "Determines if the texts of the group is displayed or not")
+ @Attributes(
+ required = false,
+ description = "Determines if the texts of the group is displayed or not")
private boolean displayText;
- @Attributes(required = false, description = "Determines if the residues text for the group is coloured")
+ @Attributes(
+ required = false,
+ description = "Determines if the residues text for the group is coloured")
private boolean colourText;
- @Attributes(required = false, description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence")
+ @Attributes(
+ required = false,
+ description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence")
private boolean showNonconserved;
- @Attributes(required = true, description = "The index of the group’s first residue in the alignment space")
+ @Attributes(
+ required = true,
+ description = "The index of the group’s first residue in the alignment space")
private int startRes;
- @Attributes(required = true, description = "The index of the group’s last residue in the alignment space")
+ @Attributes(
+ required = true,
+ description = "The index of the group’s last residue in the alignment space")
private int endRes;
-
+
@Attributes(
required = true,
minItems = 1,
this.sequenceRefs = sequenceRefs;
}
-
}
import com.github.reinert.jjschema.Attributes;
-
-
public class SequencePojo
{
@Attributes(
@Attributes(required = true, description = "Sequence name")
private String name;
- @Attributes(required = false, description = "Sequence type", enums = {"DNA", "RNA", "Protein"})
+ @Attributes(required = false, description = "Sequence type", enums = {
+ "DNA", "RNA", "Protein" })
private String type;
- @Attributes(required = true, description = "Unique identifier for a given Sequence")
+ @Attributes(
+ required = true,
+ description = "Unique identifier for a given Sequence")
private String id;
-
- @Attributes(required = false, description = "The order/position of a sequence in the alignment space")
+
+ @Attributes(
+ required = false,
+ description = "The order/position of a sequence in the alignment space")
private int order;
-
- @Attributes(required = true, description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
+
+ @Attributes(
+ required = true,
+ description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
private int start;
- @Attributes(required = true, description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
+ @Attributes(
+ required = true,
+ description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
private int end;
-
public SequencePojo()
{
}
this.name = name;
this.seq = seq;
}
+
public String getSeq()
{
return seq;
this.order = order;
}
-
public String getType()
{
return type;
*/
package jalview.math;
-import java.io.*;
+import jalview.util.Format;
+import jalview.util.MessageManager;
-import jalview.util.*;
+import java.io.PrintStream;
/**
* DOCUMENT ME!
if (iter == maxIter)
{
- throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli", Integer.valueOf(maxIter).toString()}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.matrix_too_many_iteration", new String[] {
+ "tqli", Integer.valueOf(maxIter).toString() }));
}
else
{
if (iter == maxIter)
{
- throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli2", Integer.valueOf(maxIter).toString()}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.matrix_too_many_iteration", new String[] {
+ "tqli2", Integer.valueOf(maxIter).toString() }));
}
else
{
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
- g.fillPolygon(new int[]
- { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
}
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
- g.fillPolygon(new int[]
- { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
}
if (diffupstream)
//
// if (scaleColLabel)
// {
- // justify the label and scale to fit in column
- if (fmWidth > charWidth)
- {
- // scale only if the current font isn't already small enough
- fmScaling = charWidth;
- fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform
- .getScaleInstance(fmScaling, 1.0)));
- // and update the label's width to reflect the scaling.
- fmWidth = charWidth;
- }
+ // justify the label and scale to fit in column
+ if (fmWidth > charWidth)
+ {
+ // scale only if the current font isn't already small enough
+ fmScaling = charWidth;
+ fmScaling /= fmWidth;
+ g.setFont(ofont.deriveFont(AffineTransform
+ .getScaleInstance(fmScaling, 1.0)));
+ // and update the label's width to reflect the scaling.
+ fmWidth = charWidth;
+ }
// }
}
// TODO is it ok to use width of / show all characters here?
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
- new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
- 3);
+ g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
+ (x * charWidth) }, new int[] { y + iconOffset,
+ y + 14 + iconOffset, y + 7 + iconOffset }, 3);
}
else
{
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range)
* _aa.graphHeight);
* This is used by the Molecule Viewer and Overview to get the accurate
* colourof the rendered sequence
*/
- public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
- int column)
+ public synchronized int findFeatureColour(int initialCol,
+ final SequenceI seq, int column)
{
if (!av.isShowSequenceFeatures())
{
}
if (offscreenRender && offscreenImage == null)
- {
+ {
if (sequenceFeature.begin <= start
&& sequenceFeature.end >= start)
{
package jalview.rest;
+import jalview.httpserver.AbstractRequestHandler;
+
import java.io.IOException;
import java.io.PrintWriter;
import java.net.BindException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import jalview.httpserver.AbstractRequestHandler;
-
/**
* A simple handler to process (or delegate) HTTP requests on /jalview/rest
*/
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AlcodMap implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal jalview id for the dnasq for this mapping.
- *
- */
- private java.lang.String _dnasq;
-
- /**
- * a Mapping entry and an associated protein sequence
- *
- */
- private jalview.schemabinding.version2.Mapping _mapping;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlcodMap() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'dnasq'. The field 'dnasq' has
- * the following description: internal jalview id for the dnasq
- * for this mapping.
- *
- *
- * @return the value of field 'Dnasq'.
- */
- public java.lang.String getDnasq(
- ) {
- return this._dnasq;
- }
-
- /**
- * Returns the value of field 'mapping'. The field 'mapping'
- * has the following description: a Mapping entry and an
- * associated protein sequence
- *
- *
- * @return the value of field 'Mapping'.
- */
- public jalview.schemabinding.version2.Mapping getMapping(
- ) {
- return this._mapping;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'dnasq'. The field 'dnasq' has the
- * following description: internal jalview id for the dnasq for
- * this mapping.
- *
- *
- * @param dnasq the value of field 'dnasq'.
- */
- public void setDnasq(
- final java.lang.String dnasq) {
- this._dnasq = dnasq;
- }
-
- /**
- * Sets the value of field 'mapping'. The field 'mapping' has
- * the following description: a Mapping entry and an associated
- * protein sequence
- *
- *
- * @param mapping the value of field 'mapping'.
- */
- public void setMapping(
- final jalview.schemabinding.version2.Mapping mapping) {
- this._mapping = mapping;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AlcodMap
- */
- public static jalview.schemabinding.version2.AlcodMap unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class AlcodMap implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * internal jalview id for the dnasq for this mapping.
+ *
+ */
+ private java.lang.String _dnasq;
+
+ /**
+ * a Mapping entry and an associated protein sequence
+ *
+ */
+ private jalview.schemabinding.version2.Mapping _mapping;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlcodMap()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'dnasq'. The field 'dnasq' has the following
+ * description: internal jalview id for the dnasq for this mapping.
+ *
+ *
+ * @return the value of field 'Dnasq'.
+ */
+ public java.lang.String getDnasq()
+ {
+ return this._dnasq;
+ }
+
+ /**
+ * Returns the value of field 'mapping'. The field 'mapping' has the following
+ * description: a Mapping entry and an associated protein sequence
+ *
+ *
+ * @return the value of field 'Mapping'.
+ */
+ public jalview.schemabinding.version2.Mapping getMapping()
+ {
+ return this._mapping;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'dnasq'. The field 'dnasq' has the following
+ * description: internal jalview id for the dnasq for this mapping.
+ *
+ *
+ * @param dnasq
+ * the value of field 'dnasq'.
+ */
+ public void setDnasq(final java.lang.String dnasq)
+ {
+ this._dnasq = dnasq;
+ }
+
+ /**
+ * Sets the value of field 'mapping'. The field 'mapping' has the following
+ * description: a Mapping entry and an associated protein sequence
+ *
+ *
+ * @param mapping
+ * the value of field 'mapping'.
+ */
+ public void setMapping(
+ final jalview.schemabinding.version2.Mapping mapping)
+ {
+ this._mapping = mapping;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.AlcodMap
+ */
+ public static jalview.schemabinding.version2.AlcodMap unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AlcodMap) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.AlcodMap.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Alcodon implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _pos1.
- */
- private long _pos1;
-
- /**
- * keeps track of state for field: _pos1
- */
- private boolean _has_pos1;
-
- /**
- * Field _pos2.
- */
- private long _pos2;
-
- /**
- * keeps track of state for field: _pos2
- */
- private boolean _has_pos2;
-
- /**
- * Field _pos3.
- */
- private long _pos3;
-
- /**
- * keeps track of state for field: _pos3
- */
- private boolean _has_pos3;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alcodon() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deletePos1(
- ) {
- this._has_pos1= false;
- }
-
- /**
- */
- public void deletePos2(
- ) {
- this._has_pos2= false;
- }
-
- /**
- */
- public void deletePos3(
- ) {
- this._has_pos3= false;
- }
-
- /**
- * Returns the value of field 'pos1'.
- *
- * @return the value of field 'Pos1'.
- */
- public long getPos1(
- ) {
- return this._pos1;
- }
-
- /**
- * Returns the value of field 'pos2'.
- *
- * @return the value of field 'Pos2'.
+public class Alcodon implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _pos1.
+ */
+ private long _pos1;
+
+ /**
+ * keeps track of state for field: _pos1
+ */
+ private boolean _has_pos1;
+
+ /**
+ * Field _pos2.
+ */
+ private long _pos2;
+
+ /**
+ * keeps track of state for field: _pos2
+ */
+ private boolean _has_pos2;
+
+ /**
+ * Field _pos3.
+ */
+ private long _pos3;
+
+ /**
+ * keeps track of state for field: _pos3
+ */
+ private boolean _has_pos3;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Alcodon()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public long getPos2(
- ) {
- return this._pos2;
- }
-
- /**
- * Returns the value of field 'pos3'.
- *
- * @return the value of field 'Pos3'.
- */
- public long getPos3(
- ) {
- return this._pos3;
- }
-
- /**
- * Method hasPos1.
- *
- * @return true if at least one Pos1 has been added
- */
- public boolean hasPos1(
- ) {
- return this._has_pos1;
- }
-
- /**
- * Method hasPos2.
- *
- * @return true if at least one Pos2 has been added
- */
- public boolean hasPos2(
- ) {
- return this._has_pos2;
- }
-
- /**
- * Method hasPos3.
- *
- * @return true if at least one Pos3 has been added
- */
- public boolean hasPos3(
- ) {
- return this._has_pos3;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
+ public void deletePos1()
+ {
+ this._has_pos1 = false;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'pos1'.
- *
- * @param pos1 the value of field 'pos1'.
- */
- public void setPos1(
- final long pos1) {
- this._pos1 = pos1;
- this._has_pos1 = true;
- }
-
- /**
- * Sets the value of field 'pos2'.
- *
- * @param pos2 the value of field 'pos2'.
- */
- public void setPos2(
- final long pos2) {
- this._pos2 = pos2;
- this._has_pos2 = true;
- }
-
- /**
- * Sets the value of field 'pos3'.
- *
- * @param pos3 the value of field 'pos3'.
- */
- public void setPos3(
- final long pos3) {
- this._pos3 = pos3;
- this._has_pos3 = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Alcodo
- */
- public static jalview.schemabinding.version2.Alcodon unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader);
- }
+ public void deletePos2()
+ {
+ this._has_pos2 = false;
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deletePos3()
+ {
+ this._has_pos3 = false;
+ }
+
+ /**
+ * Returns the value of field 'pos1'.
+ *
+ * @return the value of field 'Pos1'.
+ */
+ public long getPos1()
+ {
+ return this._pos1;
+ }
+
+ /**
+ * Returns the value of field 'pos2'.
+ *
+ * @return the value of field 'Pos2'.
+ */
+ public long getPos2()
+ {
+ return this._pos2;
+ }
+
+ /**
+ * Returns the value of field 'pos3'.
+ *
+ * @return the value of field 'Pos3'.
+ */
+ public long getPos3()
+ {
+ return this._pos3;
+ }
+
+ /**
+ * Method hasPos1.
+ *
+ * @return true if at least one Pos1 has been added
+ */
+ public boolean hasPos1()
+ {
+ return this._has_pos1;
+ }
+
+ /**
+ * Method hasPos2.
+ *
+ * @return true if at least one Pos2 has been added
+ */
+ public boolean hasPos2()
+ {
+ return this._has_pos2;
+ }
+
+ /**
+ * Method hasPos3.
+ *
+ * @return true if at least one Pos3 has been added
+ */
+ public boolean hasPos3()
+ {
+ return this._has_pos3;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'pos1'.
+ *
+ * @param pos1
+ * the value of field 'pos1'.
+ */
+ public void setPos1(final long pos1)
+ {
+ this._pos1 = pos1;
+ this._has_pos1 = true;
+ }
+
+ /**
+ * Sets the value of field 'pos2'.
+ *
+ * @param pos2
+ * the value of field 'pos2'.
+ */
+ public void setPos2(final long pos2)
+ {
+ this._pos2 = pos2;
+ this._has_pos2 = true;
+ }
+
+ /**
+ * Sets the value of field 'pos3'.
+ *
+ * @param pos3
+ * the value of field 'pos3'.
+ */
+ public void setPos3(final long pos3)
+ {
+ this._pos3 = pos3;
+ this._has_pos3 = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Alcodo
+ */
+ public static jalview.schemabinding.version2.Alcodon unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Alcodon.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AlcodonFrame implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _alcodonList.
- */
- private java.util.Vector _alcodonList;
-
- /**
- * Field _alcodMapList.
- */
- private java.util.Vector _alcodMapList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlcodonFrame() {
- super();
- this._alcodonList = new java.util.Vector();
- this._alcodMapList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAlcodMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodMap(
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodMapList.addElement(vAlcodMap);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodMap(
- final int index,
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodMapList.add(index, vAlcodMap);
- }
-
- /**
- *
- *
- * @param vAlcodon
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodon(
- final jalview.schemabinding.version2.Alcodon vAlcodon)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodonList.addElement(vAlcodon);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodon
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodon(
- final int index,
- final jalview.schemabinding.version2.Alcodon vAlcodon)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodonList.add(index, vAlcodon);
- }
-
- /**
- * Method enumerateAlcodMap.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.AlcodMap elements
- */
- public java.util.Enumeration enumerateAlcodMap(
- ) {
- return this._alcodMapList.elements();
- }
-
- /**
- * Method enumerateAlcodon.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Alcodon elements
- */
- public java.util.Enumeration enumerateAlcodon(
- ) {
- return this._alcodonList.elements();
- }
-
- /**
- * Method getAlcodMap.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.AlcodMap at the given index
- */
- public jalview.schemabinding.version2.AlcodMap getAlcodMap(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodMapList.size()) {
- throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);
- }
-
- /**
- * Method getAlcodMap.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.AlcodMap[] getAlcodMap(
- ) {
- jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
- return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);
- }
-
- /**
- * Method getAlcodMapCount.
- *
- * @return the size of this collection
- */
- public int getAlcodMapCount(
- ) {
- return this._alcodMapList.size();
- }
-
- /**
- * Method getAlcodon.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Alcodon at the given index
- */
- public jalview.schemabinding.version2.Alcodon getAlcodon(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodonList.size()) {
- throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
- }
-
- /**
- * Method getAlcodon.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Alcodon[] getAlcodon(
- ) {
- jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
- return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
- }
-
- /**
- * Method getAlcodonCount.
- *
- * @return the size of this collection
- */
- public int getAlcodonCount(
- ) {
- return this._alcodonList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlcodMap.
- *
- * @param vAlcodMap
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodMap(
- final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
- boolean removed = _alcodMapList.remove(vAlcodMap);
- return removed;
+public class AlcodonFrame implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _alcodonList.
+ */
+ private java.util.Vector _alcodonList;
+
+ /**
+ * Field _alcodMapList.
+ */
+ private java.util.Vector _alcodMapList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlcodonFrame()
+ {
+ super();
+ this._alcodonList = new java.util.Vector();
+ this._alcodMapList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodMapList.addElement(vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodMap(final int index,
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodMapList.add(index, vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodon(
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonList.addElement(vAlcodon);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodon(final int index,
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonList.add(index, vAlcodon);
+ }
+
+ /**
+ * Method enumerateAlcodMap.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap
+ * elements
+ */
+ public java.util.Enumeration enumerateAlcodMap()
+ {
+ return this._alcodMapList.elements();
+ }
+
+ /**
+ * Method enumerateAlcodon.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Alcodon
+ * elements
+ */
+ public java.util.Enumeration enumerateAlcodon()
+ {
+ return this._alcodonList.elements();
+ }
+
+ /**
+ * Method getAlcodMap.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.AlcodMap at the
+ * given index
+ */
+ public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodMapList.size())
+ {
+ throw new IndexOutOfBoundsException("getAlcodMap: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodMapList.size() - 1) + "]");
}
- /**
- * Method removeAlcodMapAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
- final int index) {
- java.lang.Object obj = this._alcodMapList.remove(index);
- return (jalview.schemabinding.version2.AlcodMap) obj;
- }
-
- /**
- * Method removeAlcodon.
- *
- * @param vAlcodon
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodon(
- final jalview.schemabinding.version2.Alcodon vAlcodon) {
- boolean removed = _alcodonList.remove(vAlcodon);
- return removed;
- }
-
- /**
- * Method removeAlcodonAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
- final int index) {
- java.lang.Object obj = this._alcodonList.remove(index);
- return (jalview.schemabinding.version2.Alcodon) obj;
- }
-
- /**
- */
- public void removeAllAlcodMap(
- ) {
- this._alcodMapList.clear();
+ return (jalview.schemabinding.version2.AlcodMap) _alcodMapList
+ .get(index);
+ }
+
+ /**
+ * Method getAlcodMap.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AlcodMap[] getAlcodMap()
+ {
+ jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
+ return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlcodMapCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodMapCount()
+ {
+ return this._alcodMapList.size();
+ }
+
+ /**
+ * Method getAlcodon.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Alcodon at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Alcodon getAlcodon(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size())
+ {
+ throw new IndexOutOfBoundsException("getAlcodon: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonList.size() - 1) + "]");
}
- /**
- */
- public void removeAllAlcodon(
- ) {
- this._alcodonList.clear();
+ return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+ }
+
+ /**
+ * Method getAlcodon.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Alcodon[] getAlcodon()
+ {
+ jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
+ return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlcodonCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonCount()
+ {
+ return this._alcodonList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vAlcodMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlcodMap(
- final int index,
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodMapList.size()) {
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
- }
-
- this._alcodMapList.set(index, vAlcodMap);
- }
-
- /**
- *
- *
- * @param vAlcodMapArray
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlcodMap.
+ *
+ * @param vAlcodMap
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ {
+ boolean removed = _alcodMapList.remove(vAlcodMap);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodMapAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
+ final int index)
+ {
+ java.lang.Object obj = this._alcodMapList.remove(index);
+ return (jalview.schemabinding.version2.AlcodMap) obj;
+ }
+
+ /**
+ * Method removeAlcodon.
+ *
+ * @param vAlcodon
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodon(
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ {
+ boolean removed = _alcodonList.remove(vAlcodon);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
+ final int index)
+ {
+ java.lang.Object obj = this._alcodonList.remove(index);
+ return (jalview.schemabinding.version2.Alcodon) obj;
+ }
+
+ /**
*/
- public void setAlcodMap(
- final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {
- //-- copy array
- _alcodMapList.clear();
-
- for (int i = 0; i < vAlcodMapArray.length; i++) {
- this._alcodMapList.add(vAlcodMapArray[i]);
- }
- }
+ public void removeAllAlcodMap()
+ {
+ this._alcodMapList.clear();
+ }
- /**
- *
- *
- * @param index
- * @param vAlcodon
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ /**
*/
- public void setAlcodon(
- final int index,
- final jalview.schemabinding.version2.Alcodon vAlcodon)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodonList.size()) {
- throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
- }
-
- this._alcodonList.set(index, vAlcodon);
+ public void removeAllAlcodon()
+ {
+ this._alcodonList.clear();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlcodMap(final int index,
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodMapList.size())
+ {
+ throw new IndexOutOfBoundsException("setAlcodMap: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodMapList.size() - 1) + "]");
}
- /**
- *
- *
- * @param vAlcodonArray
- */
- public void setAlcodon(
- final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {
- //-- copy array
- _alcodonList.clear();
-
- for (int i = 0; i < vAlcodonArray.length; i++) {
- this._alcodonList.add(vAlcodonArray[i]);
- }
+ this._alcodMapList.set(index, vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodMapArray
+ */
+ public void setAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)
+ {
+ // -- copy array
+ _alcodMapList.clear();
+
+ for (int i = 0; i < vAlcodMapArray.length; i++)
+ {
+ this._alcodMapList.add(vAlcodMapArray[i]);
}
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AlcodonFrame
- */
- public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlcodon(final int index,
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size())
+ {
+ throw new IndexOutOfBoundsException("setAlcodon: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonList.size() - 1) + "]");
}
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._alcodonList.set(index, vAlcodon);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonArray
+ */
+ public void setAlcodon(
+ final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)
+ {
+ // -- copy array
+ _alcodonList.clear();
+
+ for (int i = 0; i < vAlcodonArray.length; i++)
+ {
+ this._alcodonList.add(vAlcodonArray[i]);
}
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame
+ */
+ public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.AlcodonFrame.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Annotation implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _graph.
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _graphType.
- */
- private int _graphType;
-
- /**
- * keeps track of state for field: _graphType
- */
- private boolean _has_graphType;
-
- /**
- * Field _sequenceRef.
- */
- private java.lang.String _sequenceRef;
-
- /**
- * Field _groupRef.
- */
- private java.lang.String _groupRef;
-
- /**
- * Field _graphColour.
- */
- private int _graphColour;
-
- /**
- * keeps track of state for field: _graphColour
- */
- private boolean _has_graphColour;
-
- /**
- * Field _graphGroup.
- */
- private int _graphGroup;
-
- /**
- * keeps track of state for field: _graphGroup
- */
- private boolean _has_graphGroup;
-
- /**
- * height in pixels for the graph if this is a graph-type
- * annotation.
- */
- private int _graphHeight;
-
- /**
- * keeps track of state for field: _graphHeight
- */
- private boolean _has_graphHeight;
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _scoreOnly.
- */
- private boolean _scoreOnly = false;
-
- /**
- * keeps track of state for field: _scoreOnly
- */
- private boolean _has_scoreOnly;
-
- /**
- * Field _score.
- */
- private double _score;
-
- /**
- * keeps track of state for field: _score
- */
- private boolean _has_score;
-
- /**
- * Field _visible.
- */
- private boolean _visible;
-
- /**
- * keeps track of state for field: _visible
- */
- private boolean _has_visible;
-
- /**
- * Field _centreColLabels.
- */
- private boolean _centreColLabels;
-
- /**
- * keeps track of state for field: _centreColLabels
- */
- private boolean _has_centreColLabels;
-
- /**
- * Field _scaleColLabels.
- */
- private boolean _scaleColLabels;
-
- /**
- * keeps track of state for field: _scaleColLabels
- */
- private boolean _has_scaleColLabels;
-
- /**
- * Field _showAllColLabels.
- */
- private boolean _showAllColLabels;
-
- /**
- * keeps track of state for field: _showAllColLabels
- */
- private boolean _has_showAllColLabels;
-
- /**
- * is an autocalculated annotation row
- */
- private boolean _autoCalculated = false;
-
- /**
- * keeps track of state for field: _autoCalculated
- */
- private boolean _has_autoCalculated;
-
- /**
- * is to be shown below the alignment - introduced in Jalview
- * 2.8 for visualizing T-COFFEE alignment scores
- */
- private boolean _belowAlignment = true;
-
- /**
- * keeps track of state for field: _belowAlignment
- */
- private boolean _has_belowAlignment;
-
- /**
- * Optional string identifier used to group sets of annotation
- * produced by a particular calculation. Values are opaque
- * strings but have semantic meaning to Jalview's renderer,
- * data importer and calculation system.
- */
- private java.lang.String _calcId;
-
- /**
- * Field _annotationElementList.
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _thresholdLine.
- */
- private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Annotation() {
- super();
- this._annotationElementList = new java.util.Vector();
- this._propertyList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotationElement(
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationElementList.addElement(vAnnotationElement);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotationElement(
- final int index,
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationElementList.add(index, vAnnotationElement);
- }
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- */
- public void deleteAutoCalculated(
- ) {
- this._has_autoCalculated= false;
- }
-
- /**
- */
- public void deleteBelowAlignment(
- ) {
- this._has_belowAlignment= false;
- }
-
- /**
- */
- public void deleteCentreColLabels(
- ) {
- this._has_centreColLabels= false;
- }
-
- /**
- */
- public void deleteGraph(
- ) {
- this._has_graph= false;
- }
-
- /**
- */
- public void deleteGraphColour(
- ) {
- this._has_graphColour= false;
- }
-
- /**
- */
- public void deleteGraphGroup(
- ) {
- this._has_graphGroup= false;
- }
-
- /**
- */
- public void deleteGraphHeight(
- ) {
- this._has_graphHeight= false;
- }
-
- /**
- */
- public void deleteGraphType(
- ) {
- this._has_graphType= false;
- }
-
- /**
- */
- public void deleteScaleColLabels(
- ) {
- this._has_scaleColLabels= false;
- }
-
- /**
- */
- public void deleteScore(
- ) {
- this._has_score= false;
- }
-
- /**
- */
- public void deleteScoreOnly(
- ) {
- this._has_scoreOnly= false;
- }
-
- /**
- */
- public void deleteShowAllColLabels(
- ) {
- this._has_showAllColLabels= false;
- }
-
- /**
- */
- public void deleteVisible(
- ) {
- this._has_visible= false;
- }
-
- /**
- * Method enumerateAnnotationElement.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.AnnotationElement elements
- */
- public java.util.Enumeration enumerateAnnotationElement(
- ) {
- return this._annotationElementList.elements();
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.elements();
- }
-
- /**
- * Method getAnnotationElement.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.AnnotationElement at the
- * given index
- */
- public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size()) {
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);
- }
-
- /**
- * Method getAnnotationElement.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(
- ) {
- jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
- return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
- }
-
- /**
- * Method getAnnotationElementCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationElementCount(
- ) {
- return this._annotationElementList.size();
- }
-
- /**
- * Returns the value of field 'autoCalculated'. The field
- * 'autoCalculated' has the following description: is an
- * autocalculated annotation row
- *
- * @return the value of field 'AutoCalculated'.
- */
- public boolean getAutoCalculated(
- ) {
- return this._autoCalculated;
- }
-
- /**
- * Returns the value of field 'belowAlignment'. The field
- * 'belowAlignment' has the following description: is to be
- * shown below the alignment - introduced in Jalview 2.8 for
- * visualizing T-COFFEE alignment scores
- *
- * @return the value of field 'BelowAlignment'.
- */
- public boolean getBelowAlignment(
- ) {
- return this._belowAlignment;
- }
-
- /**
- * Returns the value of field 'calcId'. The field 'calcId' has
- * the following description: Optional string identifier used
- * to group sets of annotation produced by a particular
- * calculation. Values are opaque strings but have semantic
- * meaning to Jalview's renderer, data importer and calculation
- * system.
- *
- * @return the value of field 'CalcId'.
- */
- public java.lang.String getCalcId(
- ) {
- return this._calcId;
- }
-
- /**
- * Returns the value of field 'centreColLabels'.
- *
- * @return the value of field 'CentreColLabels'.
- */
- public boolean getCentreColLabels(
- ) {
- return this._centreColLabels;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean getGraph(
- ) {
- return this._graph;
- }
-
- /**
- * Returns the value of field 'graphColour'.
- *
- * @return the value of field 'GraphColour'.
- */
- public int getGraphColour(
- ) {
- return this._graphColour;
- }
-
- /**
- * Returns the value of field 'graphGroup'.
- *
- * @return the value of field 'GraphGroup'.
- */
- public int getGraphGroup(
- ) {
- return this._graphGroup;
- }
-
- /**
- * Returns the value of field 'graphHeight'. The field
- * 'graphHeight' has the following description: height in
- * pixels for the graph if this is a graph-type annotation.
- *
- * @return the value of field 'GraphHeight'.
- */
- public int getGraphHeight(
- ) {
- return this._graphHeight;
- }
-
- /**
- * Returns the value of field 'graphType'.
- *
- * @return the value of field 'GraphType'.
- */
- public int getGraphType(
- ) {
- return this._graphType;
- }
-
- /**
- * Returns the value of field 'groupRef'.
- *
- * @return the value of field 'GroupRef'.
- */
- public java.lang.String getGroupRef(
- ) {
- return this._groupRef;
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'label'.
- *
- * @return the value of field 'Label'.
- */
- public java.lang.String getLabel(
- ) {
- return this._label;
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Property at the given index
- */
- public jalview.schemabinding.version2.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Property[] getProperty(
- ) {
- jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
- return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- * Returns the value of field 'scaleColLabels'.
- *
- * @return the value of field 'ScaleColLabels'.
- */
- public boolean getScaleColLabels(
- ) {
- return this._scaleColLabels;
- }
-
- /**
- * Returns the value of field 'score'.
- *
- * @return the value of field 'Score'.
- */
- public double getScore(
- ) {
- return this._score;
- }
-
- /**
- * Returns the value of field 'scoreOnly'.
- *
- * @return the value of field 'ScoreOnly'.
- */
- public boolean getScoreOnly(
- ) {
- return this._scoreOnly;
- }
-
- /**
- * Returns the value of field 'sequenceRef'.
- *
- * @return the value of field 'SequenceRef'.
- */
- public java.lang.String getSequenceRef(
- ) {
- return this._sequenceRef;
- }
-
- /**
- * Returns the value of field 'showAllColLabels'.
- *
- * @return the value of field 'ShowAllColLabels'.
- */
- public boolean getShowAllColLabels(
- ) {
- return this._showAllColLabels;
- }
-
- /**
- * Returns the value of field 'thresholdLine'.
- *
- * @return the value of field 'ThresholdLine'.
- */
- public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
- ) {
- return this._thresholdLine;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean getVisible(
- ) {
- return this._visible;
- }
-
- /**
- * Method hasAutoCalculated.
- *
- * @return true if at least one AutoCalculated has been added
- */
- public boolean hasAutoCalculated(
- ) {
- return this._has_autoCalculated;
- }
-
- /**
- * Method hasBelowAlignment.
- *
- * @return true if at least one BelowAlignment has been added
- */
- public boolean hasBelowAlignment(
- ) {
- return this._has_belowAlignment;
- }
-
- /**
- * Method hasCentreColLabels.
- *
- * @return true if at least one CentreColLabels has been added
- */
- public boolean hasCentreColLabels(
- ) {
- return this._has_centreColLabels;
- }
-
- /**
- * Method hasGraph.
- *
- * @return true if at least one Graph has been added
- */
- public boolean hasGraph(
- ) {
- return this._has_graph;
- }
-
- /**
- * Method hasGraphColour.
- *
- * @return true if at least one GraphColour has been added
- */
- public boolean hasGraphColour(
- ) {
- return this._has_graphColour;
- }
-
- /**
- * Method hasGraphGroup.
- *
- * @return true if at least one GraphGroup has been added
- */
- public boolean hasGraphGroup(
- ) {
- return this._has_graphGroup;
- }
-
- /**
- * Method hasGraphHeight.
- *
- * @return true if at least one GraphHeight has been added
- */
- public boolean hasGraphHeight(
- ) {
- return this._has_graphHeight;
- }
-
- /**
- * Method hasGraphType.
- *
- * @return true if at least one GraphType has been added
- */
- public boolean hasGraphType(
- ) {
- return this._has_graphType;
- }
-
- /**
- * Method hasScaleColLabels.
- *
- * @return true if at least one ScaleColLabels has been added
- */
- public boolean hasScaleColLabels(
- ) {
- return this._has_scaleColLabels;
- }
-
- /**
- * Method hasScore.
- *
- * @return true if at least one Score has been added
- */
- public boolean hasScore(
- ) {
- return this._has_score;
- }
-
- /**
- * Method hasScoreOnly.
- *
- * @return true if at least one ScoreOnly has been added
- */
- public boolean hasScoreOnly(
- ) {
- return this._has_scoreOnly;
- }
-
- /**
- * Method hasShowAllColLabels.
- *
- * @return true if at least one ShowAllColLabels has been added
- */
- public boolean hasShowAllColLabels(
- ) {
- return this._has_showAllColLabels;
- }
-
- /**
- * Method hasVisible.
- *
- * @return true if at least one Visible has been added
- */
- public boolean hasVisible(
- ) {
- return this._has_visible;
- }
-
- /**
- * Returns the value of field 'autoCalculated'. The field
- * 'autoCalculated' has the following description: is an
- * autocalculated annotation row
- *
- * @return the value of field 'AutoCalculated'.
- */
- public boolean isAutoCalculated(
- ) {
- return this._autoCalculated;
- }
-
- /**
- * Returns the value of field 'belowAlignment'. The field
- * 'belowAlignment' has the following description: is to be
- * shown below the alignment - introduced in Jalview 2.8 for
- * visualizing T-COFFEE alignment scores
- *
- * @return the value of field 'BelowAlignment'.
- */
- public boolean isBelowAlignment(
- ) {
- return this._belowAlignment;
- }
-
- /**
- * Returns the value of field 'centreColLabels'.
- *
- * @return the value of field 'CentreColLabels'.
- */
- public boolean isCentreColLabels(
- ) {
- return this._centreColLabels;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean isGraph(
- ) {
- return this._graph;
- }
-
- /**
- * Returns the value of field 'scaleColLabels'.
- *
- * @return the value of field 'ScaleColLabels'.
- */
- public boolean isScaleColLabels(
- ) {
- return this._scaleColLabels;
- }
-
- /**
- * Returns the value of field 'scoreOnly'.
- *
- * @return the value of field 'ScoreOnly'.
- */
- public boolean isScoreOnly(
- ) {
- return this._scoreOnly;
- }
-
- /**
- * Returns the value of field 'showAllColLabels'.
- *
- * @return the value of field 'ShowAllColLabels'.
- */
- public boolean isShowAllColLabels(
- ) {
- return this._showAllColLabels;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean isVisible(
- ) {
- return this._visible;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllAnnotationElement(
- ) {
- this._annotationElementList.clear();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- * Method removeAnnotationElement.
- *
- * @param vAnnotationElement
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotationElement(
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
- boolean removed = _annotationElementList.remove(vAnnotationElement);
- return removed;
- }
-
- /**
- * Method removeAnnotationElementAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
- final int index) {
- java.lang.Object obj = this._annotationElementList.remove(index);
- return (jalview.schemabinding.version2.AnnotationElement) obj;
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final jalview.schemabinding.version2.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (jalview.schemabinding.version2.Property) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAnnotationElement(
- final int index,
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size()) {
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
- }
-
- this._annotationElementList.set(index, vAnnotationElement);
- }
-
- /**
- *
- *
- * @param vAnnotationElementArray
- */
- public void setAnnotationElement(
- final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {
- //-- copy array
- _annotationElementList.clear();
-
- for (int i = 0; i < vAnnotationElementArray.length; i++) {
- this._annotationElementList.add(vAnnotationElementArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'autoCalculated'. The field
- * 'autoCalculated' has the following description: is an
- * autocalculated annotation row
- *
- * @param autoCalculated the value of field 'autoCalculated'.
- */
- public void setAutoCalculated(
- final boolean autoCalculated) {
- this._autoCalculated = autoCalculated;
- this._has_autoCalculated = true;
- }
-
- /**
- * Sets the value of field 'belowAlignment'. The field
- * 'belowAlignment' has the following description: is to be
- * shown below the alignment - introduced in Jalview 2.8 for
- * visualizing T-COFFEE alignment scores
- *
- * @param belowAlignment the value of field 'belowAlignment'.
- */
- public void setBelowAlignment(
- final boolean belowAlignment) {
- this._belowAlignment = belowAlignment;
- this._has_belowAlignment = true;
- }
-
- /**
- * Sets the value of field 'calcId'. The field 'calcId' has the
- * following description: Optional string identifier used to
- * group sets of annotation produced by a particular
- * calculation. Values are opaque strings but have semantic
- * meaning to Jalview's renderer, data importer and calculation
- * system.
- *
- * @param calcId the value of field 'calcId'.
- */
- public void setCalcId(
- final java.lang.String calcId) {
- this._calcId = calcId;
- }
-
- /**
- * Sets the value of field 'centreColLabels'.
- *
- * @param centreColLabels the value of field 'centreColLabels'.
- */
- public void setCentreColLabels(
- final boolean centreColLabels) {
- this._centreColLabels = centreColLabels;
- this._has_centreColLabels = true;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'graph'.
- *
- * @param graph the value of field 'graph'.
- */
- public void setGraph(
- final boolean graph) {
- this._graph = graph;
- this._has_graph = true;
- }
-
- /**
- * Sets the value of field 'graphColour'.
- *
- * @param graphColour the value of field 'graphColour'.
- */
- public void setGraphColour(
- final int graphColour) {
- this._graphColour = graphColour;
- this._has_graphColour = true;
- }
-
- /**
- * Sets the value of field 'graphGroup'.
- *
- * @param graphGroup the value of field 'graphGroup'.
- */
- public void setGraphGroup(
- final int graphGroup) {
- this._graphGroup = graphGroup;
- this._has_graphGroup = true;
- }
-
- /**
- * Sets the value of field 'graphHeight'. The field
- * 'graphHeight' has the following description: height in
- * pixels for the graph if this is a graph-type annotation.
- *
- * @param graphHeight the value of field 'graphHeight'.
- */
- public void setGraphHeight(
- final int graphHeight) {
- this._graphHeight = graphHeight;
- this._has_graphHeight = true;
- }
-
- /**
- * Sets the value of field 'graphType'.
- *
- * @param graphType the value of field 'graphType'.
- */
- public void setGraphType(
- final int graphType) {
- this._graphType = graphType;
- this._has_graphType = true;
- }
-
- /**
- * Sets the value of field 'groupRef'.
- *
- * @param groupRef the value of field 'groupRef'.
- */
- public void setGroupRef(
- final java.lang.String groupRef) {
- this._groupRef = groupRef;
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'label'.
- *
- * @param label the value of field 'label'.
- */
- public void setLabel(
- final java.lang.String label) {
- this._label = label;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final jalview.schemabinding.version2.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'scaleColLabels'.
- *
- * @param scaleColLabels the value of field 'scaleColLabels'.
- */
- public void setScaleColLabels(
- final boolean scaleColLabels) {
- this._scaleColLabels = scaleColLabels;
- this._has_scaleColLabels = true;
- }
-
- /**
- * Sets the value of field 'score'.
- *
- * @param score the value of field 'score'.
- */
- public void setScore(
- final double score) {
- this._score = score;
- this._has_score = true;
- }
-
- /**
- * Sets the value of field 'scoreOnly'.
- *
- * @param scoreOnly the value of field 'scoreOnly'.
- */
- public void setScoreOnly(
- final boolean scoreOnly) {
- this._scoreOnly = scoreOnly;
- this._has_scoreOnly = true;
- }
-
- /**
- * Sets the value of field 'sequenceRef'.
- *
- * @param sequenceRef the value of field 'sequenceRef'.
- */
- public void setSequenceRef(
- final java.lang.String sequenceRef) {
- this._sequenceRef = sequenceRef;
- }
-
- /**
- * Sets the value of field 'showAllColLabels'.
- *
- * @param showAllColLabels the value of field 'showAllColLabels'
- */
- public void setShowAllColLabels(
- final boolean showAllColLabels) {
- this._showAllColLabels = showAllColLabels;
- this._has_showAllColLabels = true;
- }
-
- /**
- * Sets the value of field 'thresholdLine'.
- *
- * @param thresholdLine the value of field 'thresholdLine'.
- */
- public void setThresholdLine(
- final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
- this._thresholdLine = thresholdLine;
- }
-
- /**
- * Sets the value of field 'visible'.
- *
- * @param visible the value of field 'visible'.
- */
- public void setVisible(
- final boolean visible) {
- this._visible = visible;
- this._has_visible = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Annotation
- */
- public static jalview.schemabinding.version2.Annotation unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Annotation implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _sequenceRef.
+ */
+ private java.lang.String _sequenceRef;
+
+ /**
+ * Field _groupRef.
+ */
+ private java.lang.String _groupRef;
+
+ /**
+ * Field _graphColour.
+ */
+ private int _graphColour;
+
+ /**
+ * keeps track of state for field: _graphColour
+ */
+ private boolean _has_graphColour;
+
+ /**
+ * Field _graphGroup.
+ */
+ private int _graphGroup;
+
+ /**
+ * keeps track of state for field: _graphGroup
+ */
+ private boolean _has_graphGroup;
+
+ /**
+ * height in pixels for the graph if this is a graph-type annotation.
+ */
+ private int _graphHeight;
+
+ /**
+ * keeps track of state for field: _graphHeight
+ */
+ private boolean _has_graphHeight;
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _scoreOnly.
+ */
+ private boolean _scoreOnly = false;
+
+ /**
+ * keeps track of state for field: _scoreOnly
+ */
+ private boolean _has_scoreOnly;
+
+ /**
+ * Field _score.
+ */
+ private double _score;
+
+ /**
+ * keeps track of state for field: _score
+ */
+ private boolean _has_score;
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * Field _centreColLabels.
+ */
+ private boolean _centreColLabels;
+
+ /**
+ * keeps track of state for field: _centreColLabels
+ */
+ private boolean _has_centreColLabels;
+
+ /**
+ * Field _scaleColLabels.
+ */
+ private boolean _scaleColLabels;
+
+ /**
+ * keeps track of state for field: _scaleColLabels
+ */
+ private boolean _has_scaleColLabels;
+
+ /**
+ * Field _showAllColLabels.
+ */
+ private boolean _showAllColLabels;
+
+ /**
+ * keeps track of state for field: _showAllColLabels
+ */
+ private boolean _has_showAllColLabels;
+
+ /**
+ * is an autocalculated annotation row
+ */
+ private boolean _autoCalculated = false;
+
+ /**
+ * keeps track of state for field: _autoCalculated
+ */
+ private boolean _has_autoCalculated;
+
+ /**
+ * is to be shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ */
+ private boolean _belowAlignment = true;
+
+ /**
+ * keeps track of state for field: _belowAlignment
+ */
+ private boolean _has_belowAlignment;
+
+ /**
+ * Optional string identifier used to group sets of annotation produced by a
+ * particular calculation. Values are opaque strings but have semantic meaning
+ * to Jalview's renderer, data importer and calculation system.
+ */
+ private java.lang.String _calcId;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _thresholdLine.
+ */
+ private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Annotation()
+ {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ */
+ public void deleteAutoCalculated()
+ {
+ this._has_autoCalculated = false;
+ }
+
+ /**
+ */
+ public void deleteBelowAlignment()
+ {
+ this._has_belowAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteCentreColLabels()
+ {
+ this._has_centreColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteGraph()
+ {
+ this._has_graph = false;
+ }
+
+ /**
+ */
+ public void deleteGraphColour()
+ {
+ this._has_graphColour = false;
+ }
+
+ /**
+ */
+ public void deleteGraphGroup()
+ {
+ this._has_graphGroup = false;
+ }
+
+ /**
+ */
+ public void deleteGraphHeight()
+ {
+ this._has_graphHeight = false;
+ }
+
+ /**
+ */
+ public void deleteGraphType()
+ {
+ this._has_graphType = false;
+ }
+
+ /**
+ */
+ public void deleteScaleColLabels()
+ {
+ this._has_scaleColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteScore()
+ {
+ this._has_score = false;
+ }
+
+ /**
+ */
+ public void deleteScoreOnly()
+ {
+ this._has_scoreOnly = false;
+ }
+
+ /**
+ */
+ public void deleteShowAllColLabels()
+ {
+ this._has_showAllColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteVisible()
+ {
+ this._has_visible = false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Property
+ * elements
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.AnnotationElement
+ * at the given index
+ */
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+ {
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount()
+ {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean getAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean getBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId()
+ {
+ return this._calcId;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean getCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphColour'.
+ *
+ * @return the value of field 'GraphColour'.
+ */
+ public int getGraphColour()
+ {
+ return this._graphColour;
+ }
+
+ /**
+ * Returns the value of field 'graphGroup'.
+ *
+ * @return the value of field 'GraphGroup'.
+ */
+ public int getGraphGroup()
+ {
+ return this._graphGroup;
+ }
+
+ /**
+ * Returns the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @return the value of field 'GraphHeight'.
+ */
+ public int getGraphHeight()
+ {
+ return this._graphHeight;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType()
+ {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'groupRef'.
+ *
+ * @return the value of field 'GroupRef'.
+ */
+ public java.lang.String getGroupRef()
+ {
+ return this._groupRef;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Property at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Property) _propertyList
+ .get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Property[] getProperty()
+ {
+ jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+ return (jalview.schemabinding.version2.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount()
+ {
+ return this._propertyList.size();
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean getScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'score'.
+ *
+ * @return the value of field 'Score'.
+ */
+ public double getScore()
+ {
+ return this._score;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean getScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'sequenceRef'.
+ *
+ * @return the value of field 'SequenceRef'.
+ */
+ public java.lang.String getSequenceRef()
+ {
+ return this._sequenceRef;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean getShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * Returns the value of field 'thresholdLine'.
+ *
+ * @return the value of field 'ThresholdLine'.
+ */
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+ {
+ return this._thresholdLine;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ * Method hasAutoCalculated.
+ *
+ * @return true if at least one AutoCalculated has been added
+ */
+ public boolean hasAutoCalculated()
+ {
+ return this._has_autoCalculated;
+ }
+
+ /**
+ * Method hasBelowAlignment.
+ *
+ * @return true if at least one BelowAlignment has been added
+ */
+ public boolean hasBelowAlignment()
+ {
+ return this._has_belowAlignment;
+ }
+
+ /**
+ * Method hasCentreColLabels.
+ *
+ * @return true if at least one CentreColLabels has been added
+ */
+ public boolean hasCentreColLabels()
+ {
+ return this._has_centreColLabels;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphColour.
+ *
+ * @return true if at least one GraphColour has been added
+ */
+ public boolean hasGraphColour()
+ {
+ return this._has_graphColour;
+ }
+
+ /**
+ * Method hasGraphGroup.
+ *
+ * @return true if at least one GraphGroup has been added
+ */
+ public boolean hasGraphGroup()
+ {
+ return this._has_graphGroup;
+ }
+
+ /**
+ * Method hasGraphHeight.
+ *
+ * @return true if at least one GraphHeight has been added
+ */
+ public boolean hasGraphHeight()
+ {
+ return this._has_graphHeight;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType()
+ {
+ return this._has_graphType;
+ }
+
+ /**
+ * Method hasScaleColLabels.
+ *
+ * @return true if at least one ScaleColLabels has been added
+ */
+ public boolean hasScaleColLabels()
+ {
+ return this._has_scaleColLabels;
+ }
+
+ /**
+ * Method hasScore.
+ *
+ * @return true if at least one Score has been added
+ */
+ public boolean hasScore()
+ {
+ return this._has_score;
+ }
+
+ /**
+ * Method hasScoreOnly.
+ *
+ * @return true if at least one ScoreOnly has been added
+ */
+ public boolean hasScoreOnly()
+ {
+ return this._has_scoreOnly;
+ }
+
+ /**
+ * Method hasShowAllColLabels.
+ *
+ * @return true if at least one ShowAllColLabels has been added
+ */
+ public boolean hasShowAllColLabels()
+ {
+ return this._has_showAllColLabels;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean isAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean isBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean isCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean isScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean isScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean isShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement()
+ {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ */
+ public void removeAllProperty()
+ {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.schemabinding.version2.AnnotationElement) obj;
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.schemabinding.version2.Property vProperty)
+ {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Property removePropertyAt(
+ final int index)
+ {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.schemabinding.version2.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)
+ {
+ // -- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++)
+ {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @param autoCalculated
+ * the value of field 'autoCalculated'.
+ */
+ public void setAutoCalculated(final boolean autoCalculated)
+ {
+ this._autoCalculated = autoCalculated;
+ this._has_autoCalculated = true;
+ }
+
+ /**
+ * Sets the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @param belowAlignment
+ * the value of field 'belowAlignment'.
+ */
+ public void setBelowAlignment(final boolean belowAlignment)
+ {
+ this._belowAlignment = belowAlignment;
+ this._has_belowAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @param calcId
+ * the value of field 'calcId'.
+ */
+ public void setCalcId(final java.lang.String calcId)
+ {
+ this._calcId = calcId;
+ }
+
+ /**
+ * Sets the value of field 'centreColLabels'.
+ *
+ * @param centreColLabels
+ * the value of field 'centreColLabels'.
+ */
+ public void setCentreColLabels(final boolean centreColLabels)
+ {
+ this._centreColLabels = centreColLabels;
+ this._has_centreColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph
+ * the value of field 'graph'.
+ */
+ public void setGraph(final boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphColour'.
+ *
+ * @param graphColour
+ * the value of field 'graphColour'.
+ */
+ public void setGraphColour(final int graphColour)
+ {
+ this._graphColour = graphColour;
+ this._has_graphColour = true;
+ }
+
+ /**
+ * Sets the value of field 'graphGroup'.
+ *
+ * @param graphGroup
+ * the value of field 'graphGroup'.
+ */
+ public void setGraphGroup(final int graphGroup)
+ {
+ this._graphGroup = graphGroup;
+ this._has_graphGroup = true;
+ }
+
+ /**
+ * Sets the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @param graphHeight
+ * the value of field 'graphHeight'.
+ */
+ public void setGraphHeight(final int graphHeight)
+ {
+ this._graphHeight = graphHeight;
+ this._has_graphHeight = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType
+ * the value of field 'graphType'.
+ */
+ public void setGraphType(final int graphType)
+ {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'groupRef'.
+ *
+ * @param groupRef
+ * the value of field 'groupRef'.
+ */
+ public void setGroupRef(final java.lang.String groupRef)
+ {
+ this._groupRef = groupRef;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label
+ * the value of field 'label'.
+ */
+ public void setLabel(final java.lang.String label)
+ {
+ this._label = label;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.schemabinding.version2.Property[] vPropertyArray)
+ {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++)
+ {
+ this._propertyList.add(vPropertyArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'scaleColLabels'.
+ *
+ * @param scaleColLabels
+ * the value of field 'scaleColLabels'.
+ */
+ public void setScaleColLabels(final boolean scaleColLabels)
+ {
+ this._scaleColLabels = scaleColLabels;
+ this._has_scaleColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'score'.
+ *
+ * @param score
+ * the value of field 'score'.
+ */
+ public void setScore(final double score)
+ {
+ this._score = score;
+ this._has_score = true;
+ }
+
+ /**
+ * Sets the value of field 'scoreOnly'.
+ *
+ * @param scoreOnly
+ * the value of field 'scoreOnly'.
+ */
+ public void setScoreOnly(final boolean scoreOnly)
+ {
+ this._scoreOnly = scoreOnly;
+ this._has_scoreOnly = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceRef'.
+ *
+ * @param sequenceRef
+ * the value of field 'sequenceRef'.
+ */
+ public void setSequenceRef(final java.lang.String sequenceRef)
+ {
+ this._sequenceRef = sequenceRef;
+ }
+
+ /**
+ * Sets the value of field 'showAllColLabels'.
+ *
+ * @param showAllColLabels
+ * the value of field 'showAllColLabels'
+ */
+ public void setShowAllColLabels(final boolean showAllColLabels)
+ {
+ this._showAllColLabels = showAllColLabels;
+ this._has_showAllColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'thresholdLine'.
+ *
+ * @param thresholdLine
+ * the value of field 'thresholdLine'.
+ */
+ public void setThresholdLine(
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine)
+ {
+ this._thresholdLine = thresholdLine;
+ }
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible
+ * the value of field 'visible'.
+ */
+ public void setVisible(final boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Annotation
+ */
+ public static jalview.schemabinding.version2.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Annotation) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Annotation.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColourScheme implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _aboveThreshold.
- */
- private int _aboveThreshold;
-
- /**
- * keeps track of state for field: _aboveThreshold
- */
- private boolean _has_aboveThreshold;
-
- /**
- * Field _annotation.
- */
- private java.lang.String _annotation;
-
- /**
- * Field _minColour.
- */
- private int _minColour;
-
- /**
- * keeps track of state for field: _minColour
- */
- private boolean _has_minColour;
-
- /**
- * Field _maxColour.
- */
- private int _maxColour;
-
- /**
- * keeps track of state for field: _maxColour
- */
- private boolean _has_maxColour;
-
- /**
- * Field _colourScheme.
- */
- private java.lang.String _colourScheme;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _perSequence.
- */
- private boolean _perSequence;
-
- /**
- * keeps track of state for field: _perSequence
- */
- private boolean _has_perSequence;
-
- /**
- * Field _predefinedColours.
- */
- private boolean _predefinedColours;
-
- /**
- * keeps track of state for field: _predefinedColours
- */
- private boolean _has_predefinedColours;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColourScheme() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAboveThreshold(
- ) {
- this._has_aboveThreshold= false;
- }
-
- /**
- */
- public void deleteMaxColour(
- ) {
- this._has_maxColour= false;
- }
-
- /**
- */
- public void deleteMinColour(
- ) {
- this._has_minColour= false;
- }
-
- /**
- */
- public void deletePerSequence(
- ) {
- this._has_perSequence= false;
- }
-
- /**
- */
- public void deletePredefinedColours(
- ) {
- this._has_predefinedColours= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- * Returns the value of field 'aboveThreshold'.
- *
- * @return the value of field 'AboveThreshold'.
- */
- public int getAboveThreshold(
- ) {
- return this._aboveThreshold;
- }
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public java.lang.String getAnnotation(
- ) {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'colourScheme'.
- *
- * @return the value of field 'ColourScheme'.
- */
- public java.lang.String getColourScheme(
- ) {
- return this._colourScheme;
- }
-
- /**
- * Returns the value of field 'maxColour'.
- *
- * @return the value of field 'MaxColour'.
- */
- public int getMaxColour(
- ) {
- return this._maxColour;
- }
-
- /**
- * Returns the value of field 'minColour'.
- *
- * @return the value of field 'MinColour'.
- */
- public int getMinColour(
- ) {
- return this._minColour;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean getPerSequence(
- ) {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean getPredefinedColours(
- ) {
- return this._predefinedColours;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Method hasAboveThreshold.
- *
- * @return true if at least one AboveThreshold has been added
- */
- public boolean hasAboveThreshold(
- ) {
- return this._has_aboveThreshold;
- }
-
- /**
- * Method hasMaxColour.
- *
- * @return true if at least one MaxColour has been added
- */
- public boolean hasMaxColour(
- ) {
- return this._has_maxColour;
- }
-
- /**
- * Method hasMinColour.
- *
- * @return true if at least one MinColour has been added
- */
- public boolean hasMinColour(
- ) {
- return this._has_minColour;
- }
-
- /**
- * Method hasPerSequence.
- *
- * @return true if at least one PerSequence has been added
- */
- public boolean hasPerSequence(
- ) {
- return this._has_perSequence;
- }
-
- /**
- * Method hasPredefinedColours.
- *
- * @return true if at least one PredefinedColours has been added
- */
- public boolean hasPredefinedColours(
- ) {
- return this._has_predefinedColours;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean isPerSequence(
- ) {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean isPredefinedColours(
- ) {
- return this._predefinedColours;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'aboveThreshold'.
- *
- * @param aboveThreshold the value of field 'aboveThreshold'.
- */
- public void setAboveThreshold(
- final int aboveThreshold) {
- this._aboveThreshold = aboveThreshold;
- this._has_aboveThreshold = true;
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation the value of field 'annotation'.
- */
- public void setAnnotation(
- final java.lang.String annotation) {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'colourScheme'.
- *
- * @param colourScheme the value of field 'colourScheme'.
- */
- public void setColourScheme(
- final java.lang.String colourScheme) {
- this._colourScheme = colourScheme;
- }
-
- /**
- * Sets the value of field 'maxColour'.
- *
- * @param maxColour the value of field 'maxColour'.
- */
- public void setMaxColour(
- final int maxColour) {
- this._maxColour = maxColour;
- this._has_maxColour = true;
- }
-
- /**
- * Sets the value of field 'minColour'.
- *
- * @param minColour the value of field 'minColour'.
- */
- public void setMinColour(
- final int minColour) {
- this._minColour = minColour;
- this._has_minColour = true;
- }
-
- /**
- * Sets the value of field 'perSequence'.
- *
- * @param perSequence the value of field 'perSequence'.
- */
- public void setPerSequence(
- final boolean perSequence) {
- this._perSequence = perSequence;
- this._has_perSequence = true;
- }
-
- /**
- * Sets the value of field 'predefinedColours'.
- *
- * @param predefinedColours the value of field
- * 'predefinedColours'.
- */
- public void setPredefinedColours(
- final boolean predefinedColours) {
- this._predefinedColours = predefinedColours;
- this._has_predefinedColours = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AnnotationColourScheme
- */
- public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColourScheme.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class AnnotationColourScheme implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _aboveThreshold.
+ */
+ private int _aboveThreshold;
+
+ /**
+ * keeps track of state for field: _aboveThreshold
+ */
+ private boolean _has_aboveThreshold;
+
+ /**
+ * Field _annotation.
+ */
+ private java.lang.String _annotation;
+
+ /**
+ * Field _minColour.
+ */
+ private int _minColour;
+
+ /**
+ * keeps track of state for field: _minColour
+ */
+ private boolean _has_minColour;
+
+ /**
+ * Field _maxColour.
+ */
+ private int _maxColour;
+
+ /**
+ * keeps track of state for field: _maxColour
+ */
+ private boolean _has_maxColour;
+
+ /**
+ * Field _colourScheme.
+ */
+ private java.lang.String _colourScheme;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _perSequence.
+ */
+ private boolean _perSequence;
+
+ /**
+ * keeps track of state for field: _perSequence
+ */
+ private boolean _has_perSequence;
+
+ /**
+ * Field _predefinedColours.
+ */
+ private boolean _predefinedColours;
+
+ /**
+ * keeps track of state for field: _predefinedColours
+ */
+ private boolean _has_predefinedColours;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourScheme()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAboveThreshold()
+ {
+ this._has_aboveThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteMaxColour()
+ {
+ this._has_maxColour = false;
+ }
+
+ /**
+ */
+ public void deleteMinColour()
+ {
+ this._has_minColour = false;
+ }
+
+ /**
+ */
+ public void deletePerSequence()
+ {
+ this._has_perSequence = false;
+ }
+
+ /**
+ */
+ public void deletePredefinedColours()
+ {
+ this._has_predefinedColours = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Returns the value of field 'aboveThreshold'.
+ *
+ * @return the value of field 'AboveThreshold'.
+ */
+ public int getAboveThreshold()
+ {
+ return this._aboveThreshold;
+ }
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public java.lang.String getAnnotation()
+ {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'colourScheme'.
+ *
+ * @return the value of field 'ColourScheme'.
+ */
+ public java.lang.String getColourScheme()
+ {
+ return this._colourScheme;
+ }
+
+ /**
+ * Returns the value of field 'maxColour'.
+ *
+ * @return the value of field 'MaxColour'.
+ */
+ public int getMaxColour()
+ {
+ return this._maxColour;
+ }
+
+ /**
+ * Returns the value of field 'minColour'.
+ *
+ * @return the value of field 'MinColour'.
+ */
+ public int getMinColour()
+ {
+ return this._minColour;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean getPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean getPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAboveThreshold.
+ *
+ * @return true if at least one AboveThreshold has been added
+ */
+ public boolean hasAboveThreshold()
+ {
+ return this._has_aboveThreshold;
+ }
+
+ /**
+ * Method hasMaxColour.
+ *
+ * @return true if at least one MaxColour has been added
+ */
+ public boolean hasMaxColour()
+ {
+ return this._has_maxColour;
+ }
+
+ /**
+ * Method hasMinColour.
+ *
+ * @return true if at least one MinColour has been added
+ */
+ public boolean hasMinColour()
+ {
+ return this._has_minColour;
+ }
+
+ /**
+ * Method hasPerSequence.
+ *
+ * @return true if at least one PerSequence has been added
+ */
+ public boolean hasPerSequence()
+ {
+ return this._has_perSequence;
+ }
+
+ /**
+ * Method hasPredefinedColours.
+ *
+ * @return true if at least one PredefinedColours has been added
+ */
+ public boolean hasPredefinedColours()
+ {
+ return this._has_predefinedColours;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean isPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean isPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'aboveThreshold'.
+ *
+ * @param aboveThreshold
+ * the value of field 'aboveThreshold'.
+ */
+ public void setAboveThreshold(final int aboveThreshold)
+ {
+ this._aboveThreshold = aboveThreshold;
+ this._has_aboveThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation
+ * the value of field 'annotation'.
+ */
+ public void setAnnotation(final java.lang.String annotation)
+ {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'colourScheme'.
+ *
+ * @param colourScheme
+ * the value of field 'colourScheme'.
+ */
+ public void setColourScheme(final java.lang.String colourScheme)
+ {
+ this._colourScheme = colourScheme;
+ }
+
+ /**
+ * Sets the value of field 'maxColour'.
+ *
+ * @param maxColour
+ * the value of field 'maxColour'.
+ */
+ public void setMaxColour(final int maxColour)
+ {
+ this._maxColour = maxColour;
+ this._has_maxColour = true;
+ }
+
+ /**
+ * Sets the value of field 'minColour'.
+ *
+ * @param minColour
+ * the value of field 'minColour'.
+ */
+ public void setMinColour(final int minColour)
+ {
+ this._minColour = minColour;
+ this._has_minColour = true;
+ }
+
+ /**
+ * Sets the value of field 'perSequence'.
+ *
+ * @param perSequence
+ * the value of field 'perSequence'.
+ */
+ public void setPerSequence(final boolean perSequence)
+ {
+ this._perSequence = perSequence;
+ this._has_perSequence = true;
+ }
+
+ /**
+ * Sets the value of field 'predefinedColours'.
+ *
+ * @param predefinedColours
+ * the value of field 'predefinedColours'.
+ */
+ public void setPredefinedColours(final boolean predefinedColours)
+ {
+ this._predefinedColours = predefinedColours;
+ this._has_predefinedColours = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColourScheme.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColours extends AnnotationColourScheme
-implements java.io.Serializable
+public class AnnotationColours extends AnnotationColourScheme implements
+ java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColours() {
- super();
- }
-
+ public AnnotationColours()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AnnotationColourScheme
- */
- public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationElement implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _position.
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _displayCharacter.
- */
- private java.lang.String _displayCharacter;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _secondaryStructure.
- */
- private java.lang.String _secondaryStructure;
-
- /**
- * Field _value.
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElement() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deletePosition(
- ) {
- this._has_position= false;
- }
-
- /**
- */
- public void deleteValue(
- ) {
- this._has_value= false;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'displayCharacter'.
- *
- * @return the value of field 'DisplayCharacter'.
- */
- public java.lang.String getDisplayCharacter(
- ) {
- return this._displayCharacter;
- }
-
- /**
- * Returns the value of field 'position'.
- *
- * @return the value of field 'Position'.
- */
- public int getPosition(
- ) {
- return this._position;
- }
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return the value of field 'SecondaryStructure'.
- */
- public java.lang.String getSecondaryStructure(
- ) {
- return this._secondaryStructure;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public float getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasPosition.
- *
- * @return true if at least one Position has been added
- */
- public boolean hasPosition(
- ) {
- return this._has_position;
- }
-
- /**
- * Method hasValue.
- *
- * @return true if at least one Value has been added
- */
- public boolean hasValue(
- ) {
- return this._has_value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'displayCharacter'.
- *
- * @param displayCharacter the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(
- final java.lang.String displayCharacter) {
- this._displayCharacter = displayCharacter;
- }
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(
- final int position) {
- this._position = position;
- this._has_position = true;
- }
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure the value of field
- * 'secondaryStructure'.
- */
- public void setSecondaryStructure(
- final java.lang.String secondaryStructure) {
- this._secondaryStructure = secondaryStructure;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final float value) {
- this._value = value;
- this._has_value = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AnnotationElement
- */
- public static jalview.schemabinding.version2.AnnotationElement unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class AnnotationElement implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _position.
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _displayCharacter.
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure.
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationElement()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deletePosition()
+ {
+ this._has_position = false;
+ }
+
+ /**
+ */
+ public void deleteValue()
+ {
+ this._has_value = false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'displayCharacter'.
+ *
+ * @return the value of field 'DisplayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter()
+ {
+ return this._displayCharacter;
+ }
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return the value of field 'Position'.
+ */
+ public int getPosition()
+ {
+ return this._position;
+ }
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return the value of field 'SecondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure()
+ {
+ return this._secondaryStructure;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition()
+ {
+ return this._has_position;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue()
+ {
+ return this._has_value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'displayCharacter'.
+ *
+ * @param displayCharacter
+ * the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(final java.lang.String displayCharacter)
+ {
+ this._displayCharacter = displayCharacter;
+ }
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position
+ * the value of field 'position'.
+ */
+ public void setPosition(final int position)
+ {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure
+ * the value of field 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(
+ final java.lang.String secondaryStructure)
+ {
+ this._secondaryStructure = secondaryStructure;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final float value)
+ {
+ this._value = value;
+ this._has_value = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement
+ */
+ public static jalview.schemabinding.version2.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationElement.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class CalcIdParam extends WebServiceParameterSet
-implements java.io.Serializable
+public class CalcIdParam extends WebServiceParameterSet implements
+ java.io.Serializable
{
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * handle for the calculation which uses
- * this parameter set
- *
- */
- private java.lang.String _calcId;
-
- /**
- * should the calculation be performed
- * immediately after loading in order to refresh results
- *
- */
- private boolean _needsUpdate = false;
-
- /**
- * keeps track of state for field: _needsUpdate
- */
- private boolean _has_needsUpdate;
-
- /**
- * should the calculation be automatically
- * performed on edits
- *
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * handle for the calculation which uses this parameter set
+ *
+ */
+ private java.lang.String _calcId;
+
+ /**
+ * should the calculation be performed immediately after loading in order to
+ * refresh results
+ *
+ */
+ private boolean _needsUpdate = false;
+
+ /**
+ * keeps track of state for field: _needsUpdate
+ */
+ private boolean _has_needsUpdate;
+
+ /**
+ * should the calculation be automatically performed on edits
+ *
+ */
+ private boolean _autoUpdate;
+
+ /**
+ * keeps track of state for field: _autoUpdate
+ */
+ private boolean _has_autoUpdate;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public CalcIdParam()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- private boolean _autoUpdate;
-
- /**
- * keeps track of state for field: _autoUpdate
- */
- private boolean _has_autoUpdate;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public CalcIdParam() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAutoUpdate(
- ) {
- this._has_autoUpdate= false;
- }
-
- /**
- */
- public void deleteNeedsUpdate(
- ) {
- this._has_needsUpdate= false;
- }
-
- /**
- * Returns the value of field 'autoUpdate'. The field
- * 'autoUpdate' has the following description: should the
- * calculation be automatically
- * performed on edits
- *
- *
- * @return the value of field 'AutoUpdate'.
- */
- public boolean getAutoUpdate(
- ) {
- return this._autoUpdate;
- }
-
- /**
- * Returns the value of field 'calcId'. The field 'calcId' has
- * the following description: handle for the calculation which
- * uses
- * this parameter set
- *
- *
- * @return the value of field 'CalcId'.
- */
- public java.lang.String getCalcId(
- ) {
- return this._calcId;
- }
-
- /**
- * Returns the value of field 'needsUpdate'. The field
- * 'needsUpdate' has the following description: should the
- * calculation be performed
- * immediately after loading in order to refresh results
- *
- *
- * @return the value of field 'NeedsUpdate'.
- */
- public boolean getNeedsUpdate(
- ) {
- return this._needsUpdate;
- }
-
- /**
- * Method hasAutoUpdate.
- *
- * @return true if at least one AutoUpdate has been added
- */
- public boolean hasAutoUpdate(
- ) {
- return this._has_autoUpdate;
- }
-
- /**
- * Method hasNeedsUpdate.
- *
- * @return true if at least one NeedsUpdate has been added
- */
- public boolean hasNeedsUpdate(
- ) {
- return this._has_needsUpdate;
- }
-
- /**
- * Returns the value of field 'autoUpdate'. The field
- * 'autoUpdate' has the following description: should the
- * calculation be automatically
- * performed on edits
- *
- *
- * @return the value of field 'AutoUpdate'.
- */
- public boolean isAutoUpdate(
- ) {
- return this._autoUpdate;
- }
-
- /**
- * Returns the value of field 'needsUpdate'. The field
- * 'needsUpdate' has the following description: should the
- * calculation be performed
- * immediately after loading in order to refresh results
- *
- *
- * @return the value of field 'NeedsUpdate'.
- */
- public boolean isNeedsUpdate(
- ) {
- return this._needsUpdate;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'autoUpdate'. The field 'autoUpdate'
- * has the following description: should the calculation be
- * automatically
- * performed on edits
- *
- *
- * @param autoUpdate the value of field 'autoUpdate'.
- */
- public void setAutoUpdate(
- final boolean autoUpdate) {
- this._autoUpdate = autoUpdate;
- this._has_autoUpdate = true;
- }
-
- /**
- * Sets the value of field 'calcId'. The field 'calcId' has the
- * following description: handle for the calculation which uses
- * this parameter set
- *
- *
- * @param calcId the value of field 'calcId'.
- */
- public void setCalcId(
- final java.lang.String calcId) {
- this._calcId = calcId;
- }
-
- /**
- * Sets the value of field 'needsUpdate'. The field
- * 'needsUpdate' has the following description: should the
- * calculation be performed
- * immediately after loading in order to refresh results
- *
- *
- * @param needsUpdate the value of field 'needsUpdate'.
- */
- public void setNeedsUpdate(
- final boolean needsUpdate) {
- this._needsUpdate = needsUpdate;
- this._has_needsUpdate = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.CalcIdParam
- */
- public static jalview.schemabinding.version2.CalcIdParam unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller.unmarshal(jalview.schemabinding.version2.CalcIdParam.class, reader);
- }
+ public void deleteAutoUpdate()
+ {
+ this._has_autoUpdate = false;
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteNeedsUpdate()
+ {
+ this._has_needsUpdate = false;
+ }
+
+ /**
+ * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the
+ * following description: should the calculation be automatically performed on
+ * edits
+ *
+ *
+ * @return the value of field 'AutoUpdate'.
+ */
+ public boolean getAutoUpdate()
+ {
+ return this._autoUpdate;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has the following
+ * description: handle for the calculation which uses this parameter set
+ *
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId()
+ {
+ return this._calcId;
+ }
+
+ /**
+ * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the
+ * following description: should the calculation be performed immediately
+ * after loading in order to refresh results
+ *
+ *
+ * @return the value of field 'NeedsUpdate'.
+ */
+ public boolean getNeedsUpdate()
+ {
+ return this._needsUpdate;
+ }
+
+ /**
+ * Method hasAutoUpdate.
+ *
+ * @return true if at least one AutoUpdate has been added
+ */
+ public boolean hasAutoUpdate()
+ {
+ return this._has_autoUpdate;
+ }
+
+ /**
+ * Method hasNeedsUpdate.
+ *
+ * @return true if at least one NeedsUpdate has been added
+ */
+ public boolean hasNeedsUpdate()
+ {
+ return this._has_needsUpdate;
+ }
+
+ /**
+ * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the
+ * following description: should the calculation be automatically performed on
+ * edits
+ *
+ *
+ * @return the value of field 'AutoUpdate'.
+ */
+ public boolean isAutoUpdate()
+ {
+ return this._autoUpdate;
+ }
+
+ /**
+ * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the
+ * following description: should the calculation be performed immediately
+ * after loading in order to refresh results
+ *
+ *
+ * @return the value of field 'NeedsUpdate'.
+ */
+ public boolean isNeedsUpdate()
+ {
+ return this._needsUpdate;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoUpdate'. The field 'autoUpdate' has the
+ * following description: should the calculation be automatically performed on
+ * edits
+ *
+ *
+ * @param autoUpdate
+ * the value of field 'autoUpdate'.
+ */
+ public void setAutoUpdate(final boolean autoUpdate)
+ {
+ this._autoUpdate = autoUpdate;
+ this._has_autoUpdate = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the following
+ * description: handle for the calculation which uses this parameter set
+ *
+ *
+ * @param calcId
+ * the value of field 'calcId'.
+ */
+ public void setCalcId(final java.lang.String calcId)
+ {
+ this._calcId = calcId;
+ }
+
+ /**
+ * Sets the value of field 'needsUpdate'. The field 'needsUpdate' has the
+ * following description: should the calculation be performed immediately
+ * after loading in order to refresh results
+ *
+ *
+ * @param needsUpdate
+ * the value of field 'needsUpdate'.
+ */
+ public void setNeedsUpdate(final boolean needsUpdate)
+ {
+ this._needsUpdate = needsUpdate;
+ this._has_needsUpdate = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.CalcIdParam
+ */
+ public static jalview.schemabinding.version2.CalcIdParam unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.CalcIdParam.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Colour implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _RGB.
- */
- private java.lang.String _RGB;
-
- /**
- * Field _minRGB.
- */
- private java.lang.String _minRGB;
-
- /**
- * loosely specified enumeration: NONE,ABOVE, or BELOW
- */
- private java.lang.String _threshType;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _max.
- */
- private float _max;
-
- /**
- * keeps track of state for field: _max
- */
- private boolean _has_max;
-
- /**
- * Field _min.
- */
- private float _min;
-
- /**
- * keeps track of state for field: _min
- */
- private boolean _has_min;
-
- /**
- * Field _colourByLabel.
- */
- private boolean _colourByLabel;
-
- /**
- * keeps track of state for field: _colourByLabel
- */
- private boolean _has_colourByLabel;
-
- /**
- * Field _autoScale.
- */
- private boolean _autoScale;
-
- /**
- * keeps track of state for field: _autoScale
- */
- private boolean _has_autoScale;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Colour() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAutoScale(
- ) {
- this._has_autoScale= false;
- }
-
- /**
- */
- public void deleteColourByLabel(
- ) {
- this._has_colourByLabel= false;
- }
-
- /**
- */
- public void deleteMax(
- ) {
- this._has_max= false;
- }
-
- /**
- */
- public void deleteMin(
- ) {
- this._has_min= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean getAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean getColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'max'.
- *
- * @return the value of field 'Max'.
- */
- public float getMax(
- ) {
- return this._max;
- }
-
- /**
- * Returns the value of field 'min'.
- *
- * @return the value of field 'Min'.
- */
- public float getMin(
- ) {
- return this._min;
- }
-
- /**
- * Returns the value of field 'minRGB'.
- *
- * @return the value of field 'MinRGB'.
- */
- public java.lang.String getMinRGB(
- ) {
- return this._minRGB;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'RGB'.
- *
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB(
- ) {
- return this._RGB;
- }
-
- /**
- * Returns the value of field 'threshType'. The field
- * 'threshType' has the following description: loosely
- * specified enumeration: NONE,ABOVE, or BELOW
- *
- * @return the value of field 'ThreshType'.
- */
- public java.lang.String getThreshType(
- ) {
- return this._threshType;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Method hasAutoScale.
- *
- * @return true if at least one AutoScale has been added
- */
- public boolean hasAutoScale(
- ) {
- return this._has_autoScale;
- }
-
- /**
- * Method hasColourByLabel.
- *
- * @return true if at least one ColourByLabel has been added
- */
- public boolean hasColourByLabel(
- ) {
- return this._has_colourByLabel;
- }
-
- /**
- * Method hasMax.
- *
- * @return true if at least one Max has been added
- */
- public boolean hasMax(
- ) {
- return this._has_max;
- }
-
- /**
- * Method hasMin.
- *
- * @return true if at least one Min has been added
- */
- public boolean hasMin(
- ) {
- return this._has_min;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean isAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean isColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'autoScale'.
- *
- * @param autoScale the value of field 'autoScale'.
- */
- public void setAutoScale(
- final boolean autoScale) {
- this._autoScale = autoScale;
- this._has_autoScale = true;
- }
-
- /**
- * Sets the value of field 'colourByLabel'.
- *
- * @param colourByLabel the value of field 'colourByLabel'.
- */
- public void setColourByLabel(
- final boolean colourByLabel) {
- this._colourByLabel = colourByLabel;
- this._has_colourByLabel = true;
- }
-
- /**
- * Sets the value of field 'max'.
- *
- * @param max the value of field 'max'.
- */
- public void setMax(
- final float max) {
- this._max = max;
- this._has_max = true;
- }
-
- /**
- * Sets the value of field 'min'.
- *
- * @param min the value of field 'min'.
- */
- public void setMin(
- final float min) {
- this._min = min;
- this._has_min = true;
- }
-
- /**
- * Sets the value of field 'minRGB'.
- *
- * @param minRGB the value of field 'minRGB'.
- */
- public void setMinRGB(
- final java.lang.String minRGB) {
- this._minRGB = minRGB;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB the value of field 'RGB'.
- */
- public void setRGB(
- final java.lang.String RGB) {
- this._RGB = RGB;
- }
-
- /**
- * Sets the value of field 'threshType'. The field 'threshType'
- * has the following description: loosely specified
- * enumeration: NONE,ABOVE, or BELOW
- *
- * @param threshType the value of field 'threshType'.
- */
- public void setThreshType(
- final java.lang.String threshType) {
- this._threshType = threshType;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Colour
- */
- public static jalview.schemabinding.version2.Colour unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Colour implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+
+ /**
+ * loosely specified enumeration: NONE,ABOVE, or BELOW
+ */
+ private java.lang.String _threshType;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Colour()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAutoScale()
+ {
+ this._has_autoScale = false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel()
+ {
+ this._has_colourByLabel = false;
+ }
+
+ /**
+ */
+ public void deleteMax()
+ {
+ this._has_max = false;
+ }
+
+ /**
+ */
+ public void deleteMin()
+ {
+ this._has_min = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax()
+ {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin()
+ {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB()
+ {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB()
+ {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'. The field 'threshType' has the
+ * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public java.lang.String getThreshType()
+ {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale()
+ {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel()
+ {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax()
+ {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin()
+ {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale
+ * the value of field 'autoScale'.
+ */
+ public void setAutoScale(final boolean autoScale)
+ {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel
+ * the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(final boolean colourByLabel)
+ {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max
+ * the value of field 'max'.
+ */
+ public void setMax(final float max)
+ {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min
+ * the value of field 'min'.
+ */
+ public void setMin(final float min)
+ {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB
+ * the value of field 'minRGB'.
+ */
+ public void setMinRGB(final java.lang.String minRGB)
+ {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB
+ * the value of field 'RGB'.
+ */
+ public void setRGB(final java.lang.String RGB)
+ {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'. The field 'threshType' has the
+ * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @param threshType
+ * the value of field 'threshType'.
+ */
+ public void setThreshType(final java.lang.String threshType)
+ {
+ this._threshType = threshType;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Colour
+ */
+ public static jalview.schemabinding.version2.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Colour.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class DBRef implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _source.
- */
- private java.lang.String _source;
-
- /**
- * Field _version.
- */
- private java.lang.String _version;
-
- /**
- * Field _accessionId.
- */
- private java.lang.String _accessionId;
-
- /**
- * Field _mapping.
- */
- private jalview.schemabinding.version2.Mapping _mapping;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DBRef() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'accessionId'.
- *
- * @return the value of field 'AccessionId'.
- */
- public java.lang.String getAccessionId(
- ) {
- return this._accessionId;
- }
-
- /**
- * Returns the value of field 'mapping'.
- *
- * @return the value of field 'Mapping'.
- */
- public jalview.schemabinding.version2.Mapping getMapping(
- ) {
- return this._mapping;
- }
-
- /**
- * Returns the value of field 'source'.
- *
- * @return the value of field 'Source'.
- */
- public java.lang.String getSource(
- ) {
- return this._source;
- }
-
- /**
- * Returns the value of field 'version'.
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'accessionId'.
- *
- * @param accessionId the value of field 'accessionId'.
- */
- public void setAccessionId(
- final java.lang.String accessionId) {
- this._accessionId = accessionId;
- }
-
- /**
- * Sets the value of field 'mapping'.
- *
- * @param mapping the value of field 'mapping'.
- */
- public void setMapping(
- final jalview.schemabinding.version2.Mapping mapping) {
- this._mapping = mapping;
- }
-
- /**
- * Sets the value of field 'source'.
- *
- * @param source the value of field 'source'.
- */
- public void setSource(
- final java.lang.String source) {
- this._source = source;
- }
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.DBRef
- */
- public static jalview.schemabinding.version2.DBRef unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class DBRef implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _source.
+ */
+ private java.lang.String _source;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _accessionId.
+ */
+ private java.lang.String _accessionId;
+
+ /**
+ * Field _mapping.
+ */
+ private jalview.schemabinding.version2.Mapping _mapping;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DBRef()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'accessionId'.
+ *
+ * @return the value of field 'AccessionId'.
+ */
+ public java.lang.String getAccessionId()
+ {
+ return this._accessionId;
+ }
+
+ /**
+ * Returns the value of field 'mapping'.
+ *
+ * @return the value of field 'Mapping'.
+ */
+ public jalview.schemabinding.version2.Mapping getMapping()
+ {
+ return this._mapping;
+ }
+
+ /**
+ * Returns the value of field 'source'.
+ *
+ * @return the value of field 'Source'.
+ */
+ public java.lang.String getSource()
+ {
+ return this._source;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'accessionId'.
+ *
+ * @param accessionId
+ * the value of field 'accessionId'.
+ */
+ public void setAccessionId(final java.lang.String accessionId)
+ {
+ this._accessionId = accessionId;
+ }
+
+ /**
+ * Sets the value of field 'mapping'.
+ *
+ * @param mapping
+ * the value of field 'mapping'.
+ */
+ public void setMapping(
+ final jalview.schemabinding.version2.Mapping mapping)
+ {
+ this._mapping = mapping;
+ }
+
+ /**
+ * Sets the value of field 'source'.
+ *
+ * @param source
+ * the value of field 'source'.
+ */
+ public void setSource(final java.lang.String source)
+ {
+ this._source = source;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DBRef
+ */
+ public static jalview.schemabinding.version2.DBRef unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.DBRef.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Feature implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _begin.
- */
- private int _begin;
-
- /**
- * keeps track of state for field: _begin
- */
- private boolean _has_begin;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _status.
- */
- private java.lang.String _status;
-
- /**
- * Field _featureGroup.
- */
- private java.lang.String _featureGroup;
-
- /**
- * Field _score.
- */
- private float _score;
-
- /**
- * keeps track of state for field: _score
- */
- private boolean _has_score;
-
- /**
- * Field _otherDataList.
- */
- private java.util.Vector _otherDataList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Feature() {
- super();
- this._otherDataList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vOtherData
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addOtherData(
- final jalview.schemabinding.version2.OtherData vOtherData)
- throws java.lang.IndexOutOfBoundsException {
- this._otherDataList.addElement(vOtherData);
- }
-
- /**
- *
- *
- * @param index
- * @param vOtherData
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addOtherData(
- final int index,
- final jalview.schemabinding.version2.OtherData vOtherData)
- throws java.lang.IndexOutOfBoundsException {
- this._otherDataList.add(index, vOtherData);
- }
-
- /**
- */
- public void deleteBegin(
- ) {
- this._has_begin= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteScore(
- ) {
- this._has_score= false;
- }
-
- /**
- * Method enumerateOtherData.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.OtherData elements
- */
- public java.util.Enumeration enumerateOtherData(
- ) {
- return this._otherDataList.elements();
- }
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return the value of field 'Begin'.
- */
- public int getBegin(
- ) {
- return this._begin;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'featureGroup'.
- *
- * @return the value of field 'FeatureGroup'.
- */
- public java.lang.String getFeatureGroup(
- ) {
- return this._featureGroup;
- }
-
- /**
- * Method getOtherData.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.OtherData at the given index
- */
- public jalview.schemabinding.version2.OtherData getOtherData(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._otherDataList.size()) {
- throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);
- }
-
- /**
- * Method getOtherData.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.OtherData[] getOtherData(
- ) {
- jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
- return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);
- }
-
- /**
- * Method getOtherDataCount.
- *
- * @return the size of this collection
- */
- public int getOtherDataCount(
- ) {
- return this._otherDataList.size();
- }
-
- /**
- * Returns the value of field 'score'.
- *
- * @return the value of field 'Score'.
- */
- public float getScore(
- ) {
- return this._score;
- }
-
- /**
- * Returns the value of field 'status'.
- *
- * @return the value of field 'Status'.
- */
- public java.lang.String getStatus(
- ) {
- return this._status;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method hasBegin.
- *
- * @return true if at least one Begin has been added
- */
- public boolean hasBegin(
- ) {
- return this._has_begin;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasScore.
- *
- * @return true if at least one Score has been added
- */
- public boolean hasScore(
- ) {
- return this._has_score;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllOtherData(
- ) {
- this._otherDataList.clear();
- }
-
- /**
- * Method removeOtherData.
- *
- * @param vOtherData
- * @return true if the object was removed from the collection.
- */
- public boolean removeOtherData(
- final jalview.schemabinding.version2.OtherData vOtherData) {
- boolean removed = _otherDataList.remove(vOtherData);
- return removed;
- }
-
- /**
- * Method removeOtherDataAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.OtherData removeOtherDataAt(
- final int index) {
- java.lang.Object obj = this._otherDataList.remove(index);
- return (jalview.schemabinding.version2.OtherData) obj;
- }
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin the value of field 'begin'.
- */
- public void setBegin(
- final int begin) {
- this._begin = begin;
- this._has_begin = true;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'featureGroup'.
- *
- * @param featureGroup the value of field 'featureGroup'.
- */
- public void setFeatureGroup(
- final java.lang.String featureGroup) {
- this._featureGroup = featureGroup;
- }
-
- /**
- *
- *
- * @param index
- * @param vOtherData
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setOtherData(
- final int index,
- final jalview.schemabinding.version2.OtherData vOtherData)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._otherDataList.size()) {
- throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
- }
-
- this._otherDataList.set(index, vOtherData);
- }
-
- /**
- *
- *
- * @param vOtherDataArray
- */
- public void setOtherData(
- final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {
- //-- copy array
- _otherDataList.clear();
-
- for (int i = 0; i < vOtherDataArray.length; i++) {
- this._otherDataList.add(vOtherDataArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'score'.
- *
- * @param score the value of field 'score'.
- */
- public void setScore(
- final float score) {
- this._score = score;
- this._has_score = true;
- }
-
- /**
- * Sets the value of field 'status'.
- *
- * @param status the value of field 'status'.
- */
- public void setStatus(
- final java.lang.String status) {
- this._status = status;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Featur
- */
- public static jalview.schemabinding.version2.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Feature implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+ /**
+ * Field _featureGroup.
+ */
+ private java.lang.String _featureGroup;
+
+ /**
+ * Field _score.
+ */
+ private float _score;
+
+ /**
+ * keeps track of state for field: _score
+ */
+ private boolean _has_score;
+
+ /**
+ * Field _otherDataList.
+ */
+ private java.util.Vector _otherDataList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Feature()
+ {
+ super();
+ this._otherDataList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addOtherData(
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._otherDataList.addElement(vOtherData);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addOtherData(final int index,
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._otherDataList.add(index, vOtherData);
+ }
+
+ /**
+ */
+ public void deleteBegin()
+ {
+ this._has_begin = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteScore()
+ {
+ this._has_score = false;
+ }
+
+ /**
+ * Method enumerateOtherData.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.OtherData
+ * elements
+ */
+ public java.util.Enumeration enumerateOtherData()
+ {
+ return this._otherDataList.elements();
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin()
+ {
+ return this._begin;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'featureGroup'.
+ *
+ * @return the value of field 'FeatureGroup'.
+ */
+ public java.lang.String getFeatureGroup()
+ {
+ return this._featureGroup;
+ }
+
+ /**
+ * Method getOtherData.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.OtherData at the
+ * given index
+ */
+ public jalview.schemabinding.version2.OtherData getOtherData(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._otherDataList.size())
+ {
+ throw new IndexOutOfBoundsException("getOtherData: Index value '"
+ + index + "' not in range [0.."
+ + (this._otherDataList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.OtherData) _otherDataList
+ .get(index);
+ }
+
+ /**
+ * Method getOtherData.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.OtherData[] getOtherData()
+ {
+ jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
+ return (jalview.schemabinding.version2.OtherData[]) this._otherDataList
+ .toArray(array);
+ }
+
+ /**
+ * Method getOtherDataCount.
+ *
+ * @return the size of this collection
+ */
+ public int getOtherDataCount()
+ {
+ return this._otherDataList.size();
+ }
+
+ /**
+ * Returns the value of field 'score'.
+ *
+ * @return the value of field 'Score'.
+ */
+ public float getScore()
+ {
+ return this._score;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus()
+ {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin()
+ {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasScore.
+ *
+ * @return true if at least one Score has been added
+ */
+ public boolean hasScore()
+ {
+ return this._has_score;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllOtherData()
+ {
+ this._otherDataList.clear();
+ }
+
+ /**
+ * Method removeOtherData.
+ *
+ * @param vOtherData
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeOtherData(
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ {
+ boolean removed = _otherDataList.remove(vOtherData);
+ return removed;
+ }
+
+ /**
+ * Method removeOtherDataAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+ final int index)
+ {
+ java.lang.Object obj = this._otherDataList.remove(index);
+ return (jalview.schemabinding.version2.OtherData) obj;
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin
+ * the value of field 'begin'.
+ */
+ public void setBegin(final int begin)
+ {
+ this._begin = begin;
+ this._has_begin = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'featureGroup'.
+ *
+ * @param featureGroup
+ * the value of field 'featureGroup'.
+ */
+ public void setFeatureGroup(final java.lang.String featureGroup)
+ {
+ this._featureGroup = featureGroup;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setOtherData(final int index,
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._otherDataList.size())
+ {
+ throw new IndexOutOfBoundsException("setOtherData: Index value '"
+ + index + "' not in range [0.."
+ + (this._otherDataList.size() - 1) + "]");
+ }
+
+ this._otherDataList.set(index, vOtherData);
+ }
+
+ /**
+ *
+ *
+ * @param vOtherDataArray
+ */
+ public void setOtherData(
+ final jalview.schemabinding.version2.OtherData[] vOtherDataArray)
+ {
+ // -- copy array
+ _otherDataList.clear();
+
+ for (int i = 0; i < vOtherDataArray.length; i++)
+ {
+ this._otherDataList.add(vOtherDataArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'score'.
+ *
+ * @param score
+ * the value of field 'score'.
+ */
+ public void setScore(final float score)
+ {
+ this._score = score;
+ this._has_score = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status
+ * the value of field 'status'.
+ */
+ public void setStatus(final java.lang.String status)
+ {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Featur
+ */
+ public static jalview.schemabinding.version2.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Feature.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class FeatureSettings implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _settingList.
- */
- private java.util.Vector _settingList;
-
- /**
- * Field _groupList.
- */
- private java.util.Vector _groupList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public FeatureSettings() {
- super();
- this._settingList = new java.util.Vector();
- this._groupList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addGroup(
- final jalview.schemabinding.version2.Group vGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._groupList.addElement(vGroup);
- }
-
- /**
- *
- *
- * @param index
- * @param vGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addGroup(
- final int index,
- final jalview.schemabinding.version2.Group vGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._groupList.add(index, vGroup);
- }
-
- /**
- *
- *
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSetting(
- final jalview.schemabinding.version2.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- this._settingList.addElement(vSetting);
- }
-
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSetting(
- final int index,
- final jalview.schemabinding.version2.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- this._settingList.add(index, vSetting);
- }
-
- /**
- * Method enumerateGroup.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Group elements
- */
- public java.util.Enumeration enumerateGroup(
- ) {
- return this._groupList.elements();
- }
-
- /**
- * Method enumerateSetting.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Setting elements
- */
- public java.util.Enumeration enumerateSetting(
- ) {
- return this._settingList.elements();
- }
-
- /**
- * Method getGroup.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Group at the given index
- */
- public jalview.schemabinding.version2.Group getGroup(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._groupList.size()) {
- throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Group) _groupList.get(index);
- }
-
- /**
- * Method getGroup.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Group[] getGroup(
- ) {
- jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
- return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array);
- }
-
- /**
- * Method getGroupCount.
- *
- * @return the size of this collection
- */
- public int getGroupCount(
- ) {
- return this._groupList.size();
- }
-
- /**
- * Method getSetting.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Setting at the given index
- */
- public jalview.schemabinding.version2.Setting getSetting(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size()) {
- throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Setting) _settingList.get(index);
- }
-
- /**
- * Method getSetting.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Setting[] getSetting(
- ) {
- jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
- return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array);
- }
-
- /**
- * Method getSettingCount.
- *
- * @return the size of this collection
- */
- public int getSettingCount(
- ) {
- return this._settingList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllGroup(
- ) {
- this._groupList.clear();
+public class FeatureSettings implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
+
+ /**
+ * Field _groupList.
+ */
+ private java.util.Vector _groupList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public FeatureSettings()
+ {
+ super();
+ this._settingList = new java.util.Vector();
+ this._groupList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGroup(final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._groupList.addElement(vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGroup(final int index,
+ final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._groupList.add(index, vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.addElement(vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(final int index,
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.add(index, vSetting);
+ }
+
+ /**
+ * Method enumerateGroup.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Group
+ * elements
+ */
+ public java.util.Enumeration enumerateGroup()
+ {
+ return this._groupList.elements();
+ }
+
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Setting
+ * elements
+ */
+ public java.util.Enumeration enumerateSetting()
+ {
+ return this._settingList.elements();
+ }
+
+ /**
+ * Method getGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Group at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Group getGroup(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._groupList.size())
+ {
+ throw new IndexOutOfBoundsException("getGroup: Index value '" + index
+ + "' not in range [0.." + (this._groupList.size() - 1) + "]");
}
- /**
- */
- public void removeAllSetting(
- ) {
- this._settingList.clear();
- }
-
- /**
- * Method removeGroup.
- *
- * @param vGroup
- * @return true if the object was removed from the collection.
- */
- public boolean removeGroup(
- final jalview.schemabinding.version2.Group vGroup) {
- boolean removed = _groupList.remove(vGroup);
- return removed;
- }
-
- /**
- * Method removeGroupAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Group removeGroupAt(
- final int index) {
- java.lang.Object obj = this._groupList.remove(index);
- return (jalview.schemabinding.version2.Group) obj;
- }
-
- /**
- * Method removeSetting.
- *
- * @param vSetting
- * @return true if the object was removed from the collection.
- */
- public boolean removeSetting(
- final jalview.schemabinding.version2.Setting vSetting) {
- boolean removed = _settingList.remove(vSetting);
- return removed;
+ return (jalview.schemabinding.version2.Group) _groupList.get(index);
+ }
+
+ /**
+ * Method getGroup.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Group[] getGroup()
+ {
+ jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
+ return (jalview.schemabinding.version2.Group[]) this._groupList
+ .toArray(array);
+ }
+
+ /**
+ * Method getGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getGroupCount()
+ {
+ return this._groupList.size();
+ }
+
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Setting at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Setting getSetting(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("getSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
- /**
- * Method removeSettingAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Setting removeSettingAt(
- final int index) {
- java.lang.Object obj = this._settingList.remove(index);
- return (jalview.schemabinding.version2.Setting) obj;
+ return (jalview.schemabinding.version2.Setting) _settingList.get(index);
+ }
+
+ /**
+ * Method getSetting.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Setting[] getSetting()
+ {
+ jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
+ return (jalview.schemabinding.version2.Setting[]) this._settingList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount()
+ {
+ return this._settingList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setGroup(
- final int index,
- final jalview.schemabinding.version2.Group vGroup)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._groupList.size()) {
- throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
- }
-
- this._groupList.set(index, vGroup);
- }
-
- /**
- *
- *
- * @param vGroupArray
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setGroup(
- final jalview.schemabinding.version2.Group[] vGroupArray) {
- //-- copy array
- _groupList.clear();
-
- for (int i = 0; i < vGroupArray.length; i++) {
- this._groupList.add(vGroupArray[i]);
- }
- }
+ public void removeAllGroup()
+ {
+ this._groupList.clear();
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ /**
*/
- public void setSetting(
- final int index,
- final jalview.schemabinding.version2.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size()) {
- throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
- }
-
- this._settingList.set(index, vSetting);
+ public void removeAllSetting()
+ {
+ this._settingList.clear();
+ }
+
+ /**
+ * Method removeGroup.
+ *
+ * @param vGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeGroup(
+ final jalview.schemabinding.version2.Group vGroup)
+ {
+ boolean removed = _groupList.remove(vGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Group removeGroupAt(final int index)
+ {
+ java.lang.Object obj = this._groupList.remove(index);
+ return (jalview.schemabinding.version2.Group) obj;
+ }
+
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(
+ final jalview.schemabinding.version2.Setting vSetting)
+ {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
+ }
+
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Setting removeSettingAt(
+ final int index)
+ {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.schemabinding.version2.Setting) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setGroup(final int index,
+ final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._groupList.size())
+ {
+ throw new IndexOutOfBoundsException("setGroup: Index value '" + index
+ + "' not in range [0.." + (this._groupList.size() - 1) + "]");
}
- /**
- *
- *
- * @param vSettingArray
- */
- public void setSetting(
- final jalview.schemabinding.version2.Setting[] vSettingArray) {
- //-- copy array
- _settingList.clear();
-
- for (int i = 0; i < vSettingArray.length; i++) {
- this._settingList.add(vSettingArray[i]);
- }
+ this._groupList.set(index, vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vGroupArray
+ */
+ public void setGroup(
+ final jalview.schemabinding.version2.Group[] vGroupArray)
+ {
+ // -- copy array
+ _groupList.clear();
+
+ for (int i = 0; i < vGroupArray.length; i++)
+ {
+ this._groupList.add(vGroupArray[i]);
}
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.FeatureSettings
- */
- public static jalview.schemabinding.version2.FeatureSettings unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSetting(final int index,
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("setSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._settingList.set(index, vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(
+ final jalview.schemabinding.version2.Setting[] vSettingArray)
+ {
+ // -- copy array
+ _settingList.clear();
+
+ for (int i = 0; i < vSettingArray.length; i++)
+ {
+ this._settingList.add(vSettingArray[i]);
}
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings
+ */
+ public static jalview.schemabinding.version2.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.FeatureSettings.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Features extends Feature
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Features() {
- super();
- }
-
+ public Features()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Featur
- */
- public static jalview.schemabinding.version2.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Featur
+ */
+ public static jalview.schemabinding.version2.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Features.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Group implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _display.
- */
- private boolean _display;
-
- /**
- * keeps track of state for field: _display
- */
- private boolean _has_display;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Group() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteDisplay(
- ) {
- this._has_display= false;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean getDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Method hasDisplay.
- *
- * @return true if at least one Display has been added
- */
- public boolean hasDisplay(
- ) {
- return this._has_display;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean isDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'display'.
- *
- * @param display the value of field 'display'.
- */
- public void setDisplay(
- final boolean display) {
- this._display = display;
- this._has_display = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Group
- */
- public static jalview.schemabinding.version2.Group unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+public class Group implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Group()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteDisplay()
+ {
+ this._has_display = false;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay()
+ {
+ return this._has_display;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display
+ * the value of field 'display'.
+ */
+ public void setDisplay(final boolean display)
+ {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Group
+ */
+ public static jalview.schemabinding.version2.Group unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Group.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class HiddenColumns implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public HiddenColumns() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.HiddenColumns
- */
- public static jalview.schemabinding.version2.HiddenColumns unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class HiddenColumns implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public HiddenColumns()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.HiddenColumns
+ */
+ public static jalview.schemabinding.version2.HiddenColumns unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.HiddenColumns.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JGroup implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _colour.
- */
- private java.lang.String _colour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _outlineColour.
- */
- private int _outlineColour;
-
- /**
- * keeps track of state for field: _outlineColour
- */
- private boolean _has_outlineColour;
-
- /**
- * Field _displayBoxes.
- */
- private boolean _displayBoxes;
-
- /**
- * keeps track of state for field: _displayBoxes
- */
- private boolean _has_displayBoxes;
-
- /**
- * Field _displayText.
- */
- private boolean _displayText;
-
- /**
- * keeps track of state for field: _displayText
- */
- private boolean _has_displayText;
-
- /**
- * Field _colourText.
- */
- private boolean _colourText;
-
- /**
- * keeps track of state for field: _colourText
- */
- private boolean _has_colourText;
-
- /**
- * Field _textCol1.
- */
- private int _textCol1;
-
- /**
- * keeps track of state for field: _textCol1
- */
- private boolean _has_textCol1;
-
- /**
- * Field _textCol2.
- */
- private int _textCol2;
-
- /**
- * keeps track of state for field: _textCol2
- */
- private boolean _has_textCol2;
-
- /**
- * Field _textColThreshold.
- */
- private int _textColThreshold;
-
- /**
- * keeps track of state for field: _textColThreshold
- */
- private boolean _has_textColThreshold;
-
- /**
- * Field _showUnconserved.
- */
- private boolean _showUnconserved;
-
- /**
- * keeps track of state for field: _showUnconserved
- */
- private boolean _has_showUnconserved;
-
- /**
- * Field _ignoreGapsinConsensus.
- */
- private boolean _ignoreGapsinConsensus = true;
-
- /**
- * keeps track of state for field: _ignoreGapsinConsensus
- */
- private boolean _has_ignoreGapsinConsensus;
-
- /**
- * Field _showConsensusHistogram.
- */
- private boolean _showConsensusHistogram = true;
-
- /**
- * keeps track of state for field: _showConsensusHistogram
- */
- private boolean _has_showConsensusHistogram;
-
- /**
- * Field _showSequenceLogo.
- */
- private boolean _showSequenceLogo = false;
-
- /**
- * keeps track of state for field: _showSequenceLogo
- */
- private boolean _has_showSequenceLogo;
-
- /**
- * Field _normaliseSequenceLogo.
- */
- private boolean _normaliseSequenceLogo = false;
-
- /**
- * keeps track of state for field: _normaliseSequenceLogo
- */
- private boolean _has_normaliseSequenceLogo;
-
- /**
- * Optional sequence group ID (only
- * needs to be
- * unique for this
- * alignment)
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _seqList.
- */
- private java.util.Vector _seqList;
-
- /**
- * Field _annotationColours.
- */
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JGroup() {
- super();
- this._seqList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final java.lang.String vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.addElement(vSeq);
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final int index,
- final java.lang.String vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.add(index, vSeq);
- }
-
- /**
- */
- public void deleteColourText(
- ) {
- this._has_colourText= false;
- }
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteDisplayBoxes(
- ) {
- this._has_displayBoxes= false;
- }
-
- /**
- */
- public void deleteDisplayText(
- ) {
- this._has_displayText= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteIgnoreGapsinConsensus(
- ) {
- this._has_ignoreGapsinConsensus= false;
- }
-
- /**
- */
- public void deleteNormaliseSequenceLogo(
- ) {
- this._has_normaliseSequenceLogo= false;
- }
-
- /**
- */
- public void deleteOutlineColour(
- ) {
- this._has_outlineColour= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteShowConsensusHistogram(
- ) {
- this._has_showConsensusHistogram= false;
- }
-
- /**
- */
- public void deleteShowSequenceLogo(
- ) {
- this._has_showSequenceLogo= false;
- }
-
- /**
- */
- public void deleteShowUnconserved(
- ) {
- this._has_showUnconserved= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- */
- public void deleteTextCol1(
- ) {
- this._has_textCol1= false;
- }
-
- /**
- */
- public void deleteTextCol2(
- ) {
- this._has_textCol2= false;
- }
-
- /**
- */
- public void deleteTextColThreshold(
- ) {
- this._has_textColThreshold= false;
- }
-
- /**
- * Method enumerateSeq.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateSeq(
- ) {
- return this._seqList.elements();
- }
-
- /**
- * Returns the value of field 'annotationColours'.
- *
- * @return the value of field 'AnnotationColours'.
- */
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
- ) {
- return this._annotationColours;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public java.lang.String getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean getColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean getDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean getDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Optional sequence group ID (only
- * needs to be
- * unique for this
- * alignment)
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean getIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean getNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return the value of field 'OutlineColour'.
- */
- public int getOutlineColour(
- ) {
- return this._outlineColour;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Method getSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getSeq(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- return (java.lang.String) _seqList.get(index);
- }
-
- /**
- * Method getSeq.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getSeq(
- ) {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._seqList.toArray(array);
- }
-
- /**
- * Method getSeqCount.
- *
- * @return the size of this collection
- */
- public int getSeqCount(
- ) {
- return this._seqList.size();
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean getShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean getShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean getShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return the value of field 'TextCol1'.
- */
- public int getTextCol1(
- ) {
- return this._textCol1;
- }
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return the value of field 'TextCol2'.
- */
- public int getTextCol2(
- ) {
- return this._textCol2;
- }
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return the value of field 'TextColThreshold'.
- */
- public int getTextColThreshold(
- ) {
- return this._textColThreshold;
- }
-
- /**
- * Method hasColourText.
- *
- * @return true if at least one ColourText has been added
- */
- public boolean hasColourText(
- ) {
- return this._has_colourText;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasDisplayBoxes.
- *
- * @return true if at least one DisplayBoxes has been added
- */
- public boolean hasDisplayBoxes(
- ) {
- return this._has_displayBoxes;
- }
-
- /**
- * Method hasDisplayText.
- *
- * @return true if at least one DisplayText has been added
- */
- public boolean hasDisplayText(
- ) {
- return this._has_displayText;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasIgnoreGapsinConsensus.
- *
- * @return true if at least one IgnoreGapsinConsensus has been
- * added
- */
- public boolean hasIgnoreGapsinConsensus(
- ) {
- return this._has_ignoreGapsinConsensus;
- }
-
- /**
- * Method hasNormaliseSequenceLogo.
- *
- * @return true if at least one NormaliseSequenceLogo has been
- * added
- */
- public boolean hasNormaliseSequenceLogo(
- ) {
- return this._has_normaliseSequenceLogo;
- }
-
- /**
- * Method hasOutlineColour.
- *
- * @return true if at least one OutlineColour has been added
- */
- public boolean hasOutlineColour(
- ) {
- return this._has_outlineColour;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasShowConsensusHistogram.
- *
- * @return true if at least one ShowConsensusHistogram has been
- * added
- */
- public boolean hasShowConsensusHistogram(
- ) {
- return this._has_showConsensusHistogram;
- }
-
- /**
- * Method hasShowSequenceLogo.
- *
- * @return true if at least one ShowSequenceLogo has been added
- */
- public boolean hasShowSequenceLogo(
- ) {
- return this._has_showSequenceLogo;
- }
-
- /**
- * Method hasShowUnconserved.
- *
- * @return true if at least one ShowUnconserved has been added
- */
- public boolean hasShowUnconserved(
- ) {
- return this._has_showUnconserved;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Method hasTextCol1.
- *
- * @return true if at least one TextCol1 has been added
- */
- public boolean hasTextCol1(
- ) {
- return this._has_textCol1;
- }
-
- /**
- * Method hasTextCol2.
- *
- * @return true if at least one TextCol2 has been added
- */
- public boolean hasTextCol2(
- ) {
- return this._has_textCol2;
- }
-
- /**
- * Method hasTextColThreshold.
- *
- * @return true if at least one TextColThreshold has been added
- */
- public boolean hasTextColThreshold(
- ) {
- return this._has_textColThreshold;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean isColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean isDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean isDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean isIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean isNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean isShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean isShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean isShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllSeq(
- ) {
- this._seqList.clear();
- }
-
- /**
- * Method removeSeq.
- *
- * @param vSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeSeq(
- final java.lang.String vSeq) {
- boolean removed = _seqList.remove(vSeq);
- return removed;
- }
-
- /**
- * Method removeSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeSeqAt(
- final int index) {
- java.lang.Object obj = this._seqList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- * Sets the value of field 'annotationColours'.
- *
- * @param annotationColours the value of field
- * 'annotationColours'.
- */
- public void setAnnotationColours(
- final jalview.schemabinding.version2.AnnotationColours annotationColours) {
- this._annotationColours = annotationColours;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final java.lang.String colour) {
- this._colour = colour;
- }
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText the value of field 'colourText'.
- */
- public void setColourText(
- final boolean colourText) {
- this._colourText = colourText;
- this._has_colourText = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(
- final boolean displayBoxes) {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- }
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText the value of field 'displayText'.
- */
- public void setDisplayText(
- final boolean displayText) {
- this._displayText = displayText;
- this._has_displayText = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Optional sequence group ID (only
- * needs to be
- * unique for this
- * alignment)
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'ignoreGapsinConsensus'.
- *
- * @param ignoreGapsinConsensus the value of field
- * 'ignoreGapsinConsensus'.
- */
- public void setIgnoreGapsinConsensus(
- final boolean ignoreGapsinConsensus) {
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;
- this._has_ignoreGapsinConsensus = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'normaliseSequenceLogo'.
- *
- * @param normaliseSequenceLogo the value of field
- * 'normaliseSequenceLogo'.
- */
- public void setNormaliseSequenceLogo(
- final boolean normaliseSequenceLogo) {
- this._normaliseSequenceLogo = normaliseSequenceLogo;
- this._has_normaliseSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour the value of field 'outlineColour'.
- */
- public void setOutlineColour(
- final int outlineColour) {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSeq(
- final int index,
- final java.lang.String vSeq)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- this._seqList.set(index, vSeq);
- }
-
- /**
- *
- *
- * @param vSeqArray
- */
- public void setSeq(
- final java.lang.String[] vSeqArray) {
- //-- copy array
- _seqList.clear();
-
- for (int i = 0; i < vSeqArray.length; i++) {
- this._seqList.add(vSeqArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'showConsensusHistogram'.
- *
- * @param showConsensusHistogram the value of field
- * 'showConsensusHistogram'.
- */
- public void setShowConsensusHistogram(
- final boolean showConsensusHistogram) {
- this._showConsensusHistogram = showConsensusHistogram;
- this._has_showConsensusHistogram = true;
- }
-
- /**
- * Sets the value of field 'showSequenceLogo'.
- *
- * @param showSequenceLogo the value of field 'showSequenceLogo'
- */
- public void setShowSequenceLogo(
- final boolean showSequenceLogo) {
- this._showSequenceLogo = showSequenceLogo;
- this._has_showSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'showUnconserved'.
- *
- * @param showUnconserved the value of field 'showUnconserved'.
- */
- public void setShowUnconserved(
- final boolean showUnconserved) {
- this._showUnconserved = showUnconserved;
- this._has_showUnconserved = true;
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1 the value of field 'textCol1'.
- */
- public void setTextCol1(
- final int textCol1) {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- }
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2 the value of field 'textCol2'.
- */
- public void setTextCol2(
- final int textCol2) {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- }
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold the value of field 'textColThreshold'
- */
- public void setTextColThreshold(
- final int textColThreshold) {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.JGroup
- */
- public static jalview.schemabinding.version2.JGroup unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JGroup implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _textCol1.
+ */
+ private int _textCol1;
+
+ /**
+ * keeps track of state for field: _textCol1
+ */
+ private boolean _has_textCol1;
+
+ /**
+ * Field _textCol2.
+ */
+ private int _textCol2;
+
+ /**
+ * keeps track of state for field: _textCol2
+ */
+ private boolean _has_textCol2;
+
+ /**
+ * Field _textColThreshold.
+ */
+ private int _textColThreshold;
+
+ /**
+ * keeps track of state for field: _textColThreshold
+ */
+ private boolean _has_textColThreshold;
+
+ /**
+ * Field _showUnconserved.
+ */
+ private boolean _showUnconserved;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Optional sequence group ID (only needs to be unique for this alignment)
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroup()
+ {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.addElement(vSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int index, final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.add(index, vSeq);
+ }
+
+ /**
+ */
+ public void deleteColourText()
+ {
+ this._has_colourText = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes()
+ {
+ this._has_displayBoxes = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText()
+ {
+ this._has_displayText = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteIgnoreGapsinConsensus()
+ {
+ this._has_ignoreGapsinConsensus = false;
+ }
+
+ /**
+ */
+ public void deleteNormaliseSequenceLogo()
+ {
+ this._has_normaliseSequenceLogo = false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour()
+ {
+ this._has_outlineColour = false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteShowConsensusHistogram()
+ {
+ this._has_showConsensusHistogram = false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceLogo()
+ {
+ this._has_showSequenceLogo = false;
+ }
+
+ /**
+ */
+ public void deleteShowUnconserved()
+ {
+ this._has_showUnconserved = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1()
+ {
+ this._has_textCol1 = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2()
+ {
+ this._has_textCol2 = false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold()
+ {
+ this._has_textColThreshold = false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateSeq()
+ {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Optional sequence group ID (only needs to be unique for this
+ * alignment)
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour()
+ {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _seqList.get(index);
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getSeq()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._seqList.toArray(array);
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount()
+ {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1()
+ {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2()
+ {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold()
+ {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText()
+ {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes()
+ {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText()
+ {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been added
+ */
+ public boolean hasIgnoreGapsinConsensus()
+ {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been added
+ */
+ public boolean hasNormaliseSequenceLogo()
+ {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour()
+ {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been added
+ */
+ public boolean hasShowConsensusHistogram()
+ {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo()
+ {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved()
+ {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1()
+ {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2()
+ {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold()
+ {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSeq()
+ {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(final java.lang.String vSeq)
+ {
+ boolean removed = _seqList.remove(vSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeSeqAt(final int index)
+ {
+ java.lang.Object obj = this._seqList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final java.lang.String colour)
+ {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText
+ * the value of field 'colourText'.
+ */
+ public void setColourText(final boolean colourText)
+ {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes
+ * the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(final boolean displayBoxes)
+ {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText
+ * the value of field 'displayText'.
+ */
+ public void setDisplayText(final boolean displayText)
+ {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Optional sequence group ID (only needs to be unique for this alignment)
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus
+ * the value of field 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+ {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo
+ * the value of field 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+ {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour
+ * the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(final int outlineColour)
+ {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeq(final int index, final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ this._seqList.set(index, vSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(final java.lang.String[] vSeqArray)
+ {
+ // -- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++)
+ {
+ this._seqList.add(vSeqArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram
+ * the value of field 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+ {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo
+ * the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(final boolean showSequenceLogo)
+ {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved
+ * the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(final boolean showUnconserved)
+ {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1
+ * the value of field 'textCol1'.
+ */
+ public void setTextCol1(final int textCol1)
+ {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2
+ * the value of field 'textCol2'.
+ */
+ public void setTextCol2(final int textCol2)
+ {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold
+ * the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(final int textColThreshold)
+ {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JGroup
+ */
+ public static jalview.schemabinding.version2.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.JGroup.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JSeq implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _hidden.
- */
- private boolean _hidden;
-
- /**
- * keeps track of state for field: _hidden
- */
- private boolean _has_hidden;
-
- /**
- * Field _featuresList.
- */
- private java.util.Vector _featuresList;
-
- /**
- * Field _pdbidsList.
- */
- private java.util.Vector _pdbidsList;
-
- /**
- * Field _hiddenSequencesList.
- */
- private java.util.Vector _hiddenSequencesList;
-
- /**
- * Reference to a viewer showing RNA structure
- * for this sequence. Schema supports one viewer showing
- * multiple
- * annotations for multiple sequences, though currently only
- * one
- * annotation for one sequence (gapped or trimmed) is used
- *
- */
- private java.util.Vector _rnaViewerList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JSeq() {
- super();
- this._featuresList = new java.util.Vector();
- this._pdbidsList = new java.util.Vector();
- this._hiddenSequencesList = new java.util.Vector();
- this._rnaViewerList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addFeatures(
- final jalview.schemabinding.version2.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- this._featuresList.addElement(vFeatures);
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addFeatures(
- final int index,
- final jalview.schemabinding.version2.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- this._featuresList.add(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vHiddenSequences
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenSequences(
- final int vHiddenSequences)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenSequences
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenSequences(
- final int index,
- final int vHiddenSequences)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
- }
-
- /**
- *
- *
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbids(
- final jalview.schemabinding.version2.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- this._pdbidsList.addElement(vPdbids);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbids(
- final int index,
- final jalview.schemabinding.version2.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- this._pdbidsList.add(index, vPdbids);
- }
-
- /**
- *
- *
- * @param vRnaViewer
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addRnaViewer(
- final jalview.schemabinding.version2.RnaViewer vRnaViewer)
- throws java.lang.IndexOutOfBoundsException {
- this._rnaViewerList.addElement(vRnaViewer);
- }
-
- /**
- *
- *
- * @param index
- * @param vRnaViewer
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addRnaViewer(
- final int index,
- final jalview.schemabinding.version2.RnaViewer vRnaViewer)
- throws java.lang.IndexOutOfBoundsException {
- this._rnaViewerList.add(index, vRnaViewer);
- }
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteHidden(
- ) {
- this._has_hidden= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Method enumerateFeatures.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Features elements
- */
- public java.util.Enumeration enumerateFeatures(
- ) {
- return this._featuresList.elements();
- }
-
- /**
- * Method enumerateHiddenSequences.
- *
- * @return an Enumeration over all int elements
- */
- public java.util.Enumeration enumerateHiddenSequences(
- ) {
- return this._hiddenSequencesList.elements();
- }
-
- /**
- * Method enumeratePdbids.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Pdbids elements
- */
- public java.util.Enumeration enumeratePdbids(
- ) {
- return this._pdbidsList.elements();
- }
-
- /**
- * Method enumerateRnaViewer.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.RnaViewer elements
- */
- public java.util.Enumeration enumerateRnaViewer(
- ) {
- return this._rnaViewerList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Method getFeatures.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Features at the given index
- */
- public jalview.schemabinding.version2.Features getFeatures(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size()) {
- throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Features) _featuresList.get(index);
- }
-
- /**
- * Method getFeatures.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Features[] getFeatures(
- ) {
- jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
- return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);
- }
-
- /**
- * Method getFeaturesCount.
- *
- * @return the size of this collection
- */
- public int getFeaturesCount(
- ) {
- return this._featuresList.size();
- }
-
- /**
- * Returns the value of field 'hidden'.
- *
- * @return the value of field 'Hidden'.
- */
- public boolean getHidden(
- ) {
- return this._hidden;
- }
-
- /**
- * Method getHiddenSequences.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the int at the given index
- */
- public int getHiddenSequences(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenSequencesList.size()) {
- throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
- }
-
- return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
- }
-
- /**
- * Method getHiddenSequences.Returns the contents of the
- * collection in an Array.
- *
- * @return this collection as an Array
- */
- public int[] getHiddenSequences(
- ) {
- int size = this._hiddenSequencesList.size();
- int[] array = new int[size];
- java.util.Iterator iter = _hiddenSequencesList.iterator();
- for (int index = 0; index < size; index++) {
- array[index] = ((java.lang.Integer) iter.next()).intValue();
- }
- return array;
- }
-
- /**
- * Method getHiddenSequencesCount.
- *
- * @return the size of this collection
- */
- public int getHiddenSequencesCount(
- ) {
- return this._hiddenSequencesList.size();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Method getPdbids.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Pdbids at the given index
- */
- public jalview.schemabinding.version2.Pdbids getPdbids(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size()) {
- throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
- }
-
- /**
- * Method getPdbids.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Pdbids[] getPdbids(
- ) {
- jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
- return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);
- }
-
- /**
- * Method getPdbidsCount.
- *
- * @return the size of this collection
- */
- public int getPdbidsCount(
- ) {
- return this._pdbidsList.size();
- }
-
- /**
- * Method getRnaViewer.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.RnaViewer at the given index
- */
- public jalview.schemabinding.version2.RnaViewer getRnaViewer(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._rnaViewerList.size()) {
- throw new IndexOutOfBoundsException("getRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList.get(index);
- }
-
- /**
- * Method getRnaViewer.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.RnaViewer[] getRnaViewer(
- ) {
- jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
- return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList.toArray(array);
- }
-
- /**
- * Method getRnaViewerCount.
- *
- * @return the size of this collection
- */
- public int getRnaViewerCount(
- ) {
- return this._rnaViewerList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasHidden.
- *
- * @return true if at least one Hidden has been added
- */
- public boolean hasHidden(
- ) {
- return this._has_hidden;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Returns the value of field 'hidden'.
- *
- * @return the value of field 'Hidden'.
- */
- public boolean isHidden(
- ) {
- return this._hidden;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllFeatures(
- ) {
- this._featuresList.clear();
- }
-
- /**
- */
- public void removeAllHiddenSequences(
- ) {
- this._hiddenSequencesList.clear();
- }
-
- /**
- */
- public void removeAllPdbids(
- ) {
- this._pdbidsList.clear();
- }
-
- /**
- */
- public void removeAllRnaViewer(
- ) {
- this._rnaViewerList.clear();
- }
-
- /**
- * Method removeFeatures.
- *
- * @param vFeatures
- * @return true if the object was removed from the collection.
- */
- public boolean removeFeatures(
- final jalview.schemabinding.version2.Features vFeatures) {
- boolean removed = _featuresList.remove(vFeatures);
- return removed;
- }
-
- /**
- * Method removeFeaturesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Features removeFeaturesAt(
- final int index) {
- java.lang.Object obj = this._featuresList.remove(index);
- return (jalview.schemabinding.version2.Features) obj;
- }
-
- /**
- * Method removeHiddenSequences.
- *
- * @param vHiddenSequences
- * @return true if the object was removed from the collection.
- */
- public boolean removeHiddenSequences(
- final int vHiddenSequences) {
- boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
- return removed;
- }
-
- /**
- * Method removeHiddenSequencesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public int removeHiddenSequencesAt(
- final int index) {
- java.lang.Object obj = this._hiddenSequencesList.remove(index);
- return ((java.lang.Integer) obj).intValue();
- }
-
- /**
- * Method removePdbids.
- *
- * @param vPdbids
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbids(
- final jalview.schemabinding.version2.Pdbids vPdbids) {
- boolean removed = _pdbidsList.remove(vPdbids);
- return removed;
- }
-
- /**
- * Method removePdbidsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Pdbids removePdbidsAt(
- final int index) {
- java.lang.Object obj = this._pdbidsList.remove(index);
- return (jalview.schemabinding.version2.Pdbids) obj;
- }
-
- /**
- * Method removeRnaViewer.
- *
- * @param vRnaViewer
- * @return true if the object was removed from the collection.
- */
- public boolean removeRnaViewer(
- final jalview.schemabinding.version2.RnaViewer vRnaViewer) {
- boolean removed = _rnaViewerList.remove(vRnaViewer);
- return removed;
- }
-
- /**
- * Method removeRnaViewerAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
- final int index) {
- java.lang.Object obj = this._rnaViewerList.remove(index);
- return (jalview.schemabinding.version2.RnaViewer) obj;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setFeatures(
- final int index,
- final jalview.schemabinding.version2.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size()) {
- throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
- }
-
- this._featuresList.set(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vFeaturesArray
- */
- public void setFeatures(
- final jalview.schemabinding.version2.Features[] vFeaturesArray) {
- //-- copy array
- _featuresList.clear();
-
- for (int i = 0; i < vFeaturesArray.length; i++) {
- this._featuresList.add(vFeaturesArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'hidden'.
- *
- * @param hidden the value of field 'hidden'.
- */
- public void setHidden(
- final boolean hidden) {
- this._hidden = hidden;
- this._has_hidden = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenSequences
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setHiddenSequences(
- final int index,
- final int vHiddenSequences)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenSequencesList.size()) {
- throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
- }
-
- this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
- }
-
- /**
- *
- *
- * @param vHiddenSequencesArray
- */
- public void setHiddenSequences(
- final int[] vHiddenSequencesArray) {
- //-- copy array
- _hiddenSequencesList.clear();
-
- for (int i = 0; i < vHiddenSequencesArray.length; i++) {
- this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
- }
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setPdbids(
- final int index,
- final jalview.schemabinding.version2.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size()) {
- throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
- }
-
- this._pdbidsList.set(index, vPdbids);
- }
-
- /**
- *
- *
- * @param vPdbidsArray
- */
- public void setPdbids(
- final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {
- //-- copy array
- _pdbidsList.clear();
-
- for (int i = 0; i < vPdbidsArray.length; i++) {
- this._pdbidsList.add(vPdbidsArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vRnaViewer
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setRnaViewer(
- final int index,
- final jalview.schemabinding.version2.RnaViewer vRnaViewer)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._rnaViewerList.size()) {
- throw new IndexOutOfBoundsException("setRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
- }
-
- this._rnaViewerList.set(index, vRnaViewer);
- }
-
- /**
- *
- *
- * @param vRnaViewerArray
- */
- public void setRnaViewer(
- final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) {
- //-- copy array
- _rnaViewerList.clear();
-
- for (int i = 0; i < vRnaViewerArray.length; i++) {
- this._rnaViewerList.add(vRnaViewerArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.JSeq
- */
- public static jalview.schemabinding.version2.JSeq unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JSeq implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _hidden.
+ */
+ private boolean _hidden;
+
+ /**
+ * keeps track of state for field: _hidden
+ */
+ private boolean _has_hidden;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+ /**
+ * Field _hiddenSequencesList.
+ */
+ private java.util.Vector _hiddenSequencesList;
+
+ /**
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed)
+ * is used
+ *
+ */
+ private java.util.Vector _rnaViewerList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JSeq()
+ {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ this._hiddenSequencesList = new java.util.Vector();
+ this._rnaViewerList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final jalview.schemabinding.version2.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(final int index,
+ final jalview.schemabinding.version2.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenSequences(final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenSequencesList.addElement(new java.lang.Integer(
+ vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenSequences(final int index, final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenSequencesList.add(index, new java.lang.Integer(
+ vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final int index,
+ final jalview.schemabinding.version2.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rnaViewerList.addElement(vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRnaViewer(final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rnaViewerList.add(index, vRnaViewer);
+ }
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteHidden()
+ {
+ this._has_hidden = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Features
+ * elements
+ */
+ public java.util.Enumeration enumerateFeatures()
+ {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumerateHiddenSequences.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateHiddenSequences()
+ {
+ return this._hiddenSequencesList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbids()
+ {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Method enumerateRnaViewer.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
+ * elements
+ */
+ public java.util.Enumeration enumerateRnaViewer()
+ {
+ return this._rnaViewerList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Features at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Features getFeatures(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size())
+ {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Features) _featuresList
+ .get(index);
+ }
+
+ /**
+ * Method getFeatures.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Features[] getFeatures()
+ {
+ jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+ return (jalview.schemabinding.version2.Features[]) this._featuresList
+ .toArray(array);
+ }
+
+ /**
+ * Method getFeaturesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFeaturesCount()
+ {
+ return this._featuresList.size();
+ }
+
+ /**
+ * Returns the value of field 'hidden'.
+ *
+ * @return the value of field 'Hidden'.
+ */
+ public boolean getHidden()
+ {
+ return this._hidden;
+ }
+
+ /**
+ * Method getHiddenSequences.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getHiddenSequences(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenSequencesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getHiddenSequences: Index value '" + index
+ + "' not in range [0.."
+ + (this._hiddenSequencesList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+ }
+
+ /**
+ * Method getHiddenSequences.Returns the contents of the collection in an
+ * Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getHiddenSequences()
+ {
+ int size = this._hiddenSequencesList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _hiddenSequencesList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getHiddenSequencesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenSequencesCount()
+ {
+ return this._hiddenSequencesList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbids.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Pdbids at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size())
+ {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Pdbids[] getPdbids()
+ {
+ jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+ return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPdbidsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbidsCount()
+ {
+ return this._pdbidsList.size();
+ }
+
+ /**
+ * Method getRnaViewer.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.RnaViewer at the
+ * given index
+ */
+ public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
+ + index + "' not in range [0.."
+ + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
+ .get(index);
+ }
+
+ /**
+ * Method getRnaViewer.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.RnaViewer[] getRnaViewer()
+ {
+ jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+ return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
+ .toArray(array);
+ }
+
+ /**
+ * Method getRnaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getRnaViewerCount()
+ {
+ return this._rnaViewerList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasHidden.
+ *
+ * @return true if at least one Hidden has been added
+ */
+ public boolean hasHidden()
+ {
+ return this._has_hidden;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'hidden'.
+ *
+ * @return the value of field 'Hidden'.
+ */
+ public boolean isHidden()
+ {
+ return this._hidden;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllFeatures()
+ {
+ this._featuresList.clear();
+ }
+
+ /**
+ */
+ public void removeAllHiddenSequences()
+ {
+ this._hiddenSequencesList.clear();
+ }
+
+ /**
+ */
+ public void removeAllPdbids()
+ {
+ this._pdbidsList.clear();
+ }
+
+ /**
+ */
+ public void removeAllRnaViewer()
+ {
+ this._rnaViewerList.clear();
+ }
+
+ /**
+ * Method removeFeatures.
+ *
+ * @param vFeatures
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFeatures(
+ final jalview.schemabinding.version2.Features vFeatures)
+ {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Features removeFeaturesAt(
+ final int index)
+ {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.schemabinding.version2.Features) obj;
+ }
+
+ /**
+ * Method removeHiddenSequences.
+ *
+ * @param vHiddenSequences
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenSequences(final int vHiddenSequences)
+ {
+ boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
+ vHiddenSequences));
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenSequencesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeHiddenSequencesAt(final int index)
+ {
+ java.lang.Object obj = this._hiddenSequencesList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(
+ final jalview.schemabinding.version2.Pdbids vPdbids)
+ {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+ final int index)
+ {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.schemabinding.version2.Pdbids) obj;
+ }
+
+ /**
+ * Method removeRnaViewer.
+ *
+ * @param vRnaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ {
+ boolean removed = _rnaViewerList.remove(vRnaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removeRnaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+ final int index)
+ {
+ java.lang.Object obj = this._rnaViewerList.remove(index);
+ return (jalview.schemabinding.version2.RnaViewer) obj;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setFeatures(final int index,
+ final jalview.schemabinding.version2.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size())
+ {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(
+ final jalview.schemabinding.version2.Features[] vFeaturesArray)
+ {
+ // -- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++)
+ {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'hidden'.
+ *
+ * @param hidden
+ * the value of field 'hidden'.
+ */
+ public void setHidden(final boolean hidden)
+ {
+ this._hidden = hidden;
+ this._has_hidden = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setHiddenSequences(final int index, final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenSequencesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setHiddenSequences: Index value '" + index
+ + "' not in range [0.."
+ + (this._hiddenSequencesList.size() - 1) + "]");
+ }
+
+ this._hiddenSequencesList.set(index, new java.lang.Integer(
+ vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenSequencesArray
+ */
+ public void setHiddenSequences(final int[] vHiddenSequencesArray)
+ {
+ // -- copy array
+ _hiddenSequencesList.clear();
+
+ for (int i = 0; i < vHiddenSequencesArray.length; i++)
+ {
+ this._hiddenSequencesList.add(new java.lang.Integer(
+ vHiddenSequencesArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPdbids(final int index,
+ final jalview.schemabinding.version2.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size())
+ {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(
+ final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
+ {
+ // -- copy array
+ _pdbidsList.clear();
+
+ for (int i = 0; i < vPdbidsArray.length; i++)
+ {
+ this._pdbidsList.add(vPdbidsArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setRnaViewer(final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
+ + index + "' not in range [0.."
+ + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ this._rnaViewerList.set(index, vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vRnaViewerArray
+ */
+ public void setRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
+ {
+ // -- copy array
+ _rnaViewerList.clear();
+
+ for (int i = 0; i < vRnaViewerArray.length; i++)
+ {
+ this._rnaViewerList.add(vRnaViewerArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JSeq
+ */
+ public static jalview.schemabinding.version2.JSeq unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.JSeq.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModel implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _creationDate.
- */
- private java.util.Date _creationDate;
-
- /**
- * Field _version.
- */
- private java.lang.String _version;
-
- /**
- * Field _vamsasModel.
- */
- private jalview.schemabinding.version2.VamsasModel _vamsasModel;
-
- /**
- * Field _jalviewModelSequence.
- */
- private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModel() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'creationDate'.
- *
- * @return the value of field 'CreationDate'.
- */
- public java.util.Date getCreationDate(
- ) {
- return this._creationDate;
- }
-
- /**
- * Returns the value of field 'jalviewModelSequence'.
- *
- * @return the value of field 'JalviewModelSequence'.
- */
- public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence(
- ) {
- return this._jalviewModelSequence;
- }
-
- /**
- * Returns the value of field 'vamsasModel'.
- *
- * @return the value of field 'VamsasModel'.
- */
- public jalview.schemabinding.version2.VamsasModel getVamsasModel(
- ) {
- return this._vamsasModel;
- }
-
- /**
- * Returns the value of field 'version'.
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'creationDate'.
- *
- * @param creationDate the value of field 'creationDate'.
- */
- public void setCreationDate(
- final java.util.Date creationDate) {
- this._creationDate = creationDate;
- }
-
- /**
- * Sets the value of field 'jalviewModelSequence'.
- *
- * @param jalviewModelSequence the value of field
- * 'jalviewModelSequence'.
- */
- public void setJalviewModelSequence(
- final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) {
- this._jalviewModelSequence = jalviewModelSequence;
- }
-
- /**
- * Sets the value of field 'vamsasModel'.
- *
- * @param vamsasModel the value of field 'vamsasModel'.
- */
- public void setVamsasModel(
- final jalview.schemabinding.version2.VamsasModel vamsasModel) {
- this._vamsasModel = vamsasModel;
- }
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.JalviewModel
- */
- public static jalview.schemabinding.version2.JalviewModel unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _creationDate.
+ */
+ private java.util.Date _creationDate;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _vamsasModel.
+ */
+ private jalview.schemabinding.version2.VamsasModel _vamsasModel;
+
+ /**
+ * Field _jalviewModelSequence.
+ */
+ private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModel()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'creationDate'.
+ *
+ * @return the value of field 'CreationDate'.
+ */
+ public java.util.Date getCreationDate()
+ {
+ return this._creationDate;
+ }
+
+ /**
+ * Returns the value of field 'jalviewModelSequence'.
+ *
+ * @return the value of field 'JalviewModelSequence'.
+ */
+ public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
+ {
+ return this._jalviewModelSequence;
+ }
+
+ /**
+ * Returns the value of field 'vamsasModel'.
+ *
+ * @return the value of field 'VamsasModel'.
+ */
+ public jalview.schemabinding.version2.VamsasModel getVamsasModel()
+ {
+ return this._vamsasModel;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'creationDate'.
+ *
+ * @param creationDate
+ * the value of field 'creationDate'.
+ */
+ public void setCreationDate(final java.util.Date creationDate)
+ {
+ this._creationDate = creationDate;
+ }
+
+ /**
+ * Sets the value of field 'jalviewModelSequence'.
+ *
+ * @param jalviewModelSequence
+ * the value of field 'jalviewModelSequence'.
+ */
+ public void setJalviewModelSequence(
+ final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)
+ {
+ this._jalviewModelSequence = jalviewModelSequence;
+ }
+
+ /**
+ * Sets the value of field 'vamsasModel'.
+ *
+ * @param vamsasModel
+ * the value of field 'vamsasModel'.
+ */
+ public void setVamsasModel(
+ final jalview.schemabinding.version2.VamsasModel vamsasModel)
+ {
+ this._vamsasModel = vamsasModel;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JalviewModel
+ */
+ public static jalview.schemabinding.version2.JalviewModel unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewModel) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.JalviewModel.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequence implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _JSeqList.
- */
- private java.util.Vector _JSeqList;
-
- /**
- * Field _JGroupList.
- */
- private java.util.Vector _JGroupList;
-
- /**
- * Field _viewportList.
- */
- private java.util.Vector _viewportList;
-
- /**
- * Field _userColoursList.
- */
- private java.util.Vector _userColoursList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _featureSettings.
- */
- private jalview.schemabinding.version2.FeatureSettings _featureSettings;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModelSequence() {
- super();
- this._JSeqList = new java.util.Vector();
- this._JGroupList = new java.util.Vector();
- this._viewportList = new java.util.Vector();
- this._userColoursList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJGroup(
- final jalview.schemabinding.version2.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._JGroupList.addElement(vJGroup);
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJGroup(
- final int index,
- final jalview.schemabinding.version2.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- this._JGroupList.add(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJSeq(
- final jalview.schemabinding.version2.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._JSeqList.addElement(vJSeq);
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addJSeq(
- final int index,
- final jalview.schemabinding.version2.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._JSeqList.add(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final jalview.schemabinding.version2.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final jalview.schemabinding.version2.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- *
- *
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addUserColours(
- final jalview.schemabinding.version2.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- this._userColoursList.addElement(vUserColours);
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addUserColours(
- final int index,
- final jalview.schemabinding.version2.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- this._userColoursList.add(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addViewport(
- final jalview.schemabinding.version2.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- this._viewportList.addElement(vViewport);
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addViewport(
- final int index,
- final jalview.schemabinding.version2.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- this._viewportList.add(index, vViewport);
- }
-
- /**
- * Method enumerateJGroup.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.JGroup elements
- */
- public java.util.Enumeration enumerateJGroup(
- ) {
- return this._JGroupList.elements();
- }
-
- /**
- * Method enumerateJSeq.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.JSeq elements
- */
- public java.util.Enumeration enumerateJSeq(
- ) {
- return this._JSeqList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Tree elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
- }
-
- /**
- * Method enumerateUserColours.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.UserColours elements
- */
- public java.util.Enumeration enumerateUserColours(
- ) {
- return this._userColoursList.elements();
- }
-
- /**
- * Method enumerateViewport.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Viewport elements
- */
- public java.util.Enumeration enumerateViewport(
- ) {
- return this._viewportList.elements();
- }
-
- /**
- * Returns the value of field 'featureSettings'.
- *
- * @return the value of field 'FeatureSettings'.
- */
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(
- ) {
- return this._featureSettings;
- }
-
- /**
- * Method getJGroup.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.JGroup at the given index
- */
- public jalview.schemabinding.version2.JGroup getJGroup(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size()) {
- throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
- }
-
- /**
- * Method getJGroup.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.JGroup[] getJGroup(
- ) {
- jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
- return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);
- }
-
- /**
- * Method getJGroupCount.
- *
- * @return the size of this collection
- */
- public int getJGroupCount(
- ) {
- return this._JGroupList.size();
- }
-
- /**
- * Method getJSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.schemabinding.version2.JSeq
- * at the given index
- */
- public jalview.schemabinding.version2.JSeq getJSeq(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size()) {
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
- }
-
- /**
- * Method getJSeq.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.JSeq[] getJSeq(
- ) {
- jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
- return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);
- }
-
- /**
- * Method getJSeqCount.
- *
- * @return the size of this collection
- */
- public int getJSeqCount(
- ) {
- return this._JSeqList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the jalview.schemabinding.version2.Tree
- * at the given index
- */
- public jalview.schemabinding.version2.Tree getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Tree[] getTree(
- ) {
- jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
- return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Method getUserColours.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.UserColours at the given index
- */
- public jalview.schemabinding.version2.UserColours getUserColours(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size()) {
- throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);
- }
-
- /**
- * Method getUserColours.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.UserColours[] getUserColours(
- ) {
- jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
- return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);
- }
-
- /**
- * Method getUserColoursCount.
- *
- * @return the size of this collection
- */
- public int getUserColoursCount(
- ) {
- return this._userColoursList.size();
- }
-
- /**
- * Method getViewport.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Viewport at the given index
- */
- public jalview.schemabinding.version2.Viewport getViewport(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size()) {
- throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);
- }
-
- /**
- * Method getViewport.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Viewport[] getViewport(
- ) {
- jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
- return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);
- }
-
- /**
- * Method getViewportCount.
- *
- * @return the size of this collection
- */
- public int getViewportCount(
- ) {
- return this._viewportList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllJGroup(
- ) {
- this._JGroupList.clear();
- }
-
- /**
- */
- public void removeAllJSeq(
- ) {
- this._JSeqList.clear();
- }
-
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- */
- public void removeAllUserColours(
- ) {
- this._userColoursList.clear();
- }
-
- /**
- */
- public void removeAllViewport(
- ) {
- this._viewportList.clear();
- }
-
- /**
- * Method removeJGroup.
- *
- * @param vJGroup
- * @return true if the object was removed from the collection.
- */
- public boolean removeJGroup(
- final jalview.schemabinding.version2.JGroup vJGroup) {
- boolean removed = _JGroupList.remove(vJGroup);
- return removed;
- }
-
- /**
- * Method removeJGroupAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.JGroup removeJGroupAt(
- final int index) {
- java.lang.Object obj = this._JGroupList.remove(index);
- return (jalview.schemabinding.version2.JGroup) obj;
- }
-
- /**
- * Method removeJSeq.
- *
- * @param vJSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeJSeq(
- final jalview.schemabinding.version2.JSeq vJSeq) {
- boolean removed = _JSeqList.remove(vJSeq);
- return removed;
- }
-
- /**
- * Method removeJSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.JSeq removeJSeqAt(
- final int index) {
- java.lang.Object obj = this._JSeqList.remove(index);
- return (jalview.schemabinding.version2.JSeq) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final jalview.schemabinding.version2.Tree vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Tree removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (jalview.schemabinding.version2.Tree) obj;
- }
-
- /**
- * Method removeUserColours.
- *
- * @param vUserColours
- * @return true if the object was removed from the collection.
- */
- public boolean removeUserColours(
- final jalview.schemabinding.version2.UserColours vUserColours) {
- boolean removed = _userColoursList.remove(vUserColours);
- return removed;
- }
-
- /**
- * Method removeUserColoursAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.UserColours removeUserColoursAt(
- final int index) {
- java.lang.Object obj = this._userColoursList.remove(index);
- return (jalview.schemabinding.version2.UserColours) obj;
- }
-
- /**
- * Method removeViewport.
- *
- * @param vViewport
- * @return true if the object was removed from the collection.
- */
- public boolean removeViewport(
- final jalview.schemabinding.version2.Viewport vViewport) {
- boolean removed = _viewportList.remove(vViewport);
- return removed;
- }
-
- /**
- * Method removeViewportAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Viewport removeViewportAt(
- final int index) {
- java.lang.Object obj = this._viewportList.remove(index);
- return (jalview.schemabinding.version2.Viewport) obj;
- }
-
- /**
- * Sets the value of field 'featureSettings'.
- *
- * @param featureSettings the value of field 'featureSettings'.
- */
- public void setFeatureSettings(
- final jalview.schemabinding.version2.FeatureSettings featureSettings) {
- this._featureSettings = featureSettings;
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setJGroup(
- final int index,
- final jalview.schemabinding.version2.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size()) {
- throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
- }
-
- this._JGroupList.set(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJGroupArray
- */
- public void setJGroup(
- final jalview.schemabinding.version2.JGroup[] vJGroupArray) {
- //-- copy array
- _JGroupList.clear();
-
- for (int i = 0; i < vJGroupArray.length; i++) {
- this._JGroupList.add(vJGroupArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setJSeq(
- final int index,
- final jalview.schemabinding.version2.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size()) {
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- this._JSeqList.set(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vJSeqArray
- */
- public void setJSeq(
- final jalview.schemabinding.version2.JSeq[] vJSeqArray) {
- //-- copy array
- _JSeqList.clear();
-
- for (int i = 0; i < vJSeqArray.length; i++) {
- this._JSeqList.add(vJSeqArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTree(
- final int index,
- final jalview.schemabinding.version2.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final jalview.schemabinding.version2.Tree[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setUserColours(
- final int index,
- final jalview.schemabinding.version2.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size()) {
- throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
- }
-
- this._userColoursList.set(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vUserColoursArray
- */
- public void setUserColours(
- final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {
- //-- copy array
- _userColoursList.clear();
-
- for (int i = 0; i < vUserColoursArray.length; i++) {
- this._userColoursList.add(vUserColoursArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setViewport(
- final int index,
- final jalview.schemabinding.version2.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size()) {
- throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
- }
-
- this._viewportList.set(index, vViewport);
- }
-
- /**
- *
- *
- * @param vViewportArray
- */
- public void setViewport(
- final jalview.schemabinding.version2.Viewport[] vViewportArray) {
- //-- copy array
- _viewportList.clear();
-
- for (int i = 0; i < vViewportArray.length; i++) {
- this._viewportList.add(vViewportArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.JalviewModelSequence
- */
- public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModelSequence()
+ {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final int index,
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final int index,
+ final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index,
+ final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(final int index,
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(final int index,
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup()
+ {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.JSeq
+ * elements
+ */
+ public java.util.Enumeration enumerateJSeq()
+ {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Tree
+ * elements
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours()
+ {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport()
+ {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+ {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.JGroup at the given
+ * index
+ */
+ public jalview.schemabinding.version2.JGroup getJGroup(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.JGroup[] getJGroup()
+ {
+ jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+ return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
+ .toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount()
+ {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.JSeq at the given
+ * index
+ */
+ public jalview.schemabinding.version2.JSeq getJSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.JSeq[] getJSeq()
+ {
+ jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+ return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
+ .toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount()
+ {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Tree at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Tree[] getTree()
+ {
+ jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+ return (jalview.schemabinding.version2.Tree[]) this._treeList
+ .toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount()
+ {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.UserColours at the
+ * given index
+ */
+ public jalview.schemabinding.version2.UserColours getUserColours(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.UserColours) _userColoursList
+ .get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.UserColours[] getUserColours()
+ {
+ jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+ return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
+ .toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount()
+ {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Viewport at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Viewport getViewport(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("getViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Viewport) _viewportList
+ .get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Viewport[] getViewport()
+ {
+ jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+ return (jalview.schemabinding.version2.Viewport[]) this._viewportList
+ .toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount()
+ {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup()
+ {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq()
+ {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours()
+ {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport()
+ {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.JGroup removeJGroupAt(
+ final int index)
+ {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.schemabinding.version2.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+ {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
+ {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.schemabinding.version2.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
+ {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
+ {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.schemabinding.version2.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+ final int index)
+ {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.schemabinding.version2.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.schemabinding.version2.Viewport vViewport)
+ {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Viewport removeViewportAt(
+ final int index)
+ {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.schemabinding.version2.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings
+ * the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.schemabinding.version2.FeatureSettings featureSettings)
+ {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJGroup(final int index,
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.schemabinding.version2.JGroup[] vJGroupArray)
+ {
+ // -- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++)
+ {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJSeq(final int index,
+ final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+ {
+ // -- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++)
+ {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index,
+ final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+ {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++)
+ {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setUserColours(final int index,
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
+ {
+ // -- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++)
+ {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setViewport(final int index,
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("setViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.schemabinding.version2.Viewport[] vViewportArray)
+ {
+ // -- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++)
+ {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
+ */
+ public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.JalviewModelSequence.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewUserColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _schemeName.
- */
- private java.lang.String _schemeName;
-
- /**
- * Jalview colour scheme document version.
- *
- */
- private java.lang.String _version;
-
- /**
- * Field _colourList.
- */
- private java.util.Vector _colourList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewUserColours() {
- super();
- this._colourList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addColour(
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- this._colourList.addElement(vColour);
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addColour(
- final int index,
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- this._colourList.add(index, vColour);
- }
-
- /**
- * Method enumerateColour.
- *
- * @return an Enumeration over all Colour elements
- */
- public java.util.Enumeration enumerateColour(
- ) {
- return this._colourList.elements();
- }
-
- /**
- * Method getColour.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the Colour at the given index
- */
- public Colour getColour(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size()) {
- throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
- }
-
- return (Colour) _colourList.get(index);
- }
-
- /**
- * Method getColour.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public Colour[] getColour(
- ) {
- Colour[] array = new Colour[0];
- return (Colour[]) this._colourList.toArray(array);
- }
-
- /**
- * Method getColourCount.
- *
- * @return the size of this collection
- */
- public int getColourCount(
- ) {
- return this._colourList.size();
- }
-
- /**
- * Returns the value of field 'schemeName'.
- *
- * @return the value of field 'SchemeName'.
- */
- public java.lang.String getSchemeName(
- ) {
- return this._schemeName;
- }
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Jalview colour scheme
- * document version.
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllColour(
- ) {
- this._colourList.clear();
- }
-
- /**
- * Method removeColour.
- *
- * @param vColour
- * @return true if the object was removed from the collection.
- */
- public boolean removeColour(
- final Colour vColour) {
- boolean removed = _colourList.remove(vColour);
- return removed;
+public class JalviewUserColours implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewUserColours()
+ {
+ super();
+ this._colourList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour()
+ {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException("getColour: Index value '"
+ + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
- /**
- * Method removeColourAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Colour removeColourAt(
- final int index) {
- java.lang.Object obj = this._colourList.remove(index);
- return (Colour) obj;
+ return (Colour) _colourList.get(index);
+ }
+
+ /**
+ * Method getColour.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Colour[] getColour()
+ {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
+ */
+ public int getColourCount()
+ {
+ return this._colourList.size();
+ }
+
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName()
+ {
+ return this._schemeName;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setColour(
- final int index,
- final Colour vColour)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size()) {
- throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
- }
-
- this._colourList.set(index, vColour);
+ public void removeAllColour()
+ {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(final Colour vColour)
+ {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(final int index)
+ {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException("setColour: Index value '"
+ + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
- /**
- *
- *
- * @param vColourArray
- */
- public void setColour(
- final Colour[] vColourArray) {
- //-- copy array
- _colourList.clear();
-
- for (int i = 0; i < vColourArray.length; i++) {
- this._colourList.add(vColourArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'schemeName'.
- *
- * @param schemeName the value of field 'schemeName'.
- */
- public void setSchemeName(
- final java.lang.String schemeName) {
- this._schemeName = schemeName;
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Jalview colour scheme document
- * version.
- *
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.JalviewUserColours
- */
- public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(final Colour[] vColourArray)
+ {
+ // -- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++)
+ {
+ this._colourList.add(vColourArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName
+ * the value of field 'schemeName'.
+ */
+ public void setSchemeName(final java.lang.String schemeName)
+ {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+ */
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.JalviewUserColours.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class MapListFrom implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListFrom() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.MapListFrom
- */
- public static jalview.schemabinding.version2.MapListFrom unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class MapListFrom implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListFrom()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.MapListFrom
+ */
+ public static jalview.schemabinding.version2.MapListFrom unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.MapListFrom) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.MapListFrom.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class MapListTo implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListTo() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.MapListTo
- */
- public static jalview.schemabinding.version2.MapListTo unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class MapListTo implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListTo()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.MapListTo
+ */
+ public static jalview.schemabinding.version2.MapListTo unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.MapListTo) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.MapListTo.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* developed after mapRangeType from
* http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
- *
- * This effectively represents a java.util.MapList object
- *
+ *
+ * This effectively represents a java.util.MapList object
+ *
*
* @version $Revision$ $Date$
*/
-public class MapListType implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * number of dictionary symbol widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- */
- private long _mapFromUnit;
-
- /**
- * keeps track of state for field: _mapFromUnit
- */
- private boolean _has_mapFromUnit;
-
- /**
- * number of dictionary symbol widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- */
- private long _mapToUnit;
-
- /**
- * keeps track of state for field: _mapToUnit
- */
- private boolean _has_mapToUnit;
-
- /**
- * a region from start to end inclusive
- */
- private java.util.Vector _mapListFromList;
-
- /**
- * a region from start to end inclusive
- */
- private java.util.Vector _mapListToList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListType() {
- super();
- this._mapListFromList = new java.util.Vector();
- this._mapListToList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vMapListFrom
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMapListFrom(
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)
- throws java.lang.IndexOutOfBoundsException {
- this._mapListFromList.addElement(vMapListFrom);
- }
-
- /**
- *
- *
- * @param index
- * @param vMapListFrom
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMapListFrom(
- final int index,
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)
- throws java.lang.IndexOutOfBoundsException {
- this._mapListFromList.add(index, vMapListFrom);
- }
-
- /**
- *
- *
- * @param vMapListTo
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMapListTo(
- final jalview.schemabinding.version2.MapListTo vMapListTo)
- throws java.lang.IndexOutOfBoundsException {
- this._mapListToList.addElement(vMapListTo);
- }
-
- /**
- *
- *
- * @param index
- * @param vMapListTo
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMapListTo(
- final int index,
- final jalview.schemabinding.version2.MapListTo vMapListTo)
- throws java.lang.IndexOutOfBoundsException {
- this._mapListToList.add(index, vMapListTo);
- }
-
- /**
- */
- public void deleteMapFromUnit(
- ) {
- this._has_mapFromUnit= false;
- }
-
- /**
- */
- public void deleteMapToUnit(
- ) {
- this._has_mapToUnit= false;
- }
-
- /**
- * Method enumerateMapListFrom.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.MapListFrom elements
- */
- public java.util.Enumeration enumerateMapListFrom(
- ) {
- return this._mapListFromList.elements();
- }
-
- /**
- * Method enumerateMapListTo.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.MapListTo elements
- */
- public java.util.Enumeration enumerateMapListTo(
- ) {
- return this._mapListToList.elements();
- }
-
- /**
- * Returns the value of field 'mapFromUnit'. The field
- * 'mapFromUnit' has the following description: number of
- * dictionary symbol widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- * @return the value of field 'MapFromUnit'.
- */
- public long getMapFromUnit(
- ) {
- return this._mapFromUnit;
- }
-
- /**
- * Method getMapListFrom.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.MapListFrom at the given index
- */
- public jalview.schemabinding.version2.MapListFrom getMapListFrom(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapListFromList.size()) {
- throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);
- }
-
- /**
- * Method getMapListFrom.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(
- ) {
- jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
- return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);
- }
-
- /**
- * Method getMapListFromCount.
- *
- * @return the size of this collection
- */
- public int getMapListFromCount(
- ) {
- return this._mapListFromList.size();
- }
-
- /**
- * Method getMapListTo.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.MapListTo at the given index
- */
- public jalview.schemabinding.version2.MapListTo getMapListTo(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapListToList.size()) {
- throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);
- }
-
- /**
- * Method getMapListTo.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.MapListTo[] getMapListTo(
- ) {
- jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
- return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);
- }
-
- /**
- * Method getMapListToCount.
- *
- * @return the size of this collection
- */
- public int getMapListToCount(
- ) {
- return this._mapListToList.size();
- }
-
- /**
- * Returns the value of field 'mapToUnit'. The field
- * 'mapToUnit' has the following description: number of
- * dictionary symbol widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- * @return the value of field 'MapToUnit'.
- */
- public long getMapToUnit(
- ) {
- return this._mapToUnit;
- }
-
- /**
- * Method hasMapFromUnit.
- *
- * @return true if at least one MapFromUnit has been added
- */
- public boolean hasMapFromUnit(
- ) {
- return this._has_mapFromUnit;
- }
-
- /**
- * Method hasMapToUnit.
- *
- * @return true if at least one MapToUnit has been added
- */
- public boolean hasMapToUnit(
- ) {
- return this._has_mapToUnit;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllMapListFrom(
- ) {
- this._mapListFromList.clear();
- }
-
- /**
- */
- public void removeAllMapListTo(
- ) {
- this._mapListToList.clear();
- }
-
- /**
- * Method removeMapListFrom.
- *
- * @param vMapListFrom
- * @return true if the object was removed from the collection.
- */
- public boolean removeMapListFrom(
- final jalview.schemabinding.version2.MapListFrom vMapListFrom) {
- boolean removed = _mapListFromList.remove(vMapListFrom);
- return removed;
- }
-
- /**
- * Method removeMapListFromAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
- final int index) {
- java.lang.Object obj = this._mapListFromList.remove(index);
- return (jalview.schemabinding.version2.MapListFrom) obj;
- }
-
- /**
- * Method removeMapListTo.
- *
- * @param vMapListTo
- * @return true if the object was removed from the collection.
- */
- public boolean removeMapListTo(
- final jalview.schemabinding.version2.MapListTo vMapListTo) {
- boolean removed = _mapListToList.remove(vMapListTo);
- return removed;
- }
-
- /**
- * Method removeMapListToAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.MapListTo removeMapListToAt(
- final int index) {
- java.lang.Object obj = this._mapListToList.remove(index);
- return (jalview.schemabinding.version2.MapListTo) obj;
- }
-
- /**
- * Sets the value of field 'mapFromUnit'. The field
- * 'mapFromUnit' has the following description: number of
- * dictionary symbol widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- * @param mapFromUnit the value of field 'mapFromUnit'.
- */
- public void setMapFromUnit(
- final long mapFromUnit) {
- this._mapFromUnit = mapFromUnit;
- this._has_mapFromUnit = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vMapListFrom
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setMapListFrom(
- final int index,
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapListFromList.size()) {
- throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
- }
-
- this._mapListFromList.set(index, vMapListFrom);
- }
-
- /**
- *
- *
- * @param vMapListFromArray
- */
- public void setMapListFrom(
- final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {
- //-- copy array
- _mapListFromList.clear();
-
- for (int i = 0; i < vMapListFromArray.length; i++) {
- this._mapListFromList.add(vMapListFromArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vMapListTo
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setMapListTo(
- final int index,
- final jalview.schemabinding.version2.MapListTo vMapListTo)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapListToList.size()) {
- throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
- }
-
- this._mapListToList.set(index, vMapListTo);
- }
-
- /**
- *
- *
- * @param vMapListToArray
- */
- public void setMapListTo(
- final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {
- //-- copy array
- _mapListToList.clear();
-
- for (int i = 0; i < vMapListToArray.length; i++) {
- this._mapListToList.add(vMapListToArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'mapToUnit'. The field 'mapToUnit'
- * has the following description: number of dictionary symbol
- * widths involved in each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence). This is
- * optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- * @param mapToUnit the value of field 'mapToUnit'.
- */
- public void setMapToUnit(
- final long mapToUnit) {
- this._mapToUnit = mapToUnit;
- this._has_mapToUnit = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.MapListType
- */
- public static jalview.schemabinding.version2.MapListType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class MapListType implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ */
+ private long _mapFromUnit;
+
+ /**
+ * keeps track of state for field: _mapFromUnit
+ */
+ private boolean _has_mapFromUnit;
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ */
+ private long _mapToUnit;
+
+ /**
+ * keeps track of state for field: _mapToUnit
+ */
+ private boolean _has_mapToUnit;
+
+ /**
+ * a region from start to end inclusive
+ */
+ private java.util.Vector _mapListFromList;
+
+ /**
+ * a region from start to end inclusive
+ */
+ private java.util.Vector _mapListToList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListType()
+ {
+ super();
+ this._mapListFromList = new java.util.Vector();
+ this._mapListToList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vMapListFrom
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMapListFrom(
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._mapListFromList.addElement(vMapListFrom);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMapListFrom
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMapListFrom(final int index,
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._mapListFromList.add(index, vMapListFrom);
+ }
+
+ /**
+ *
+ *
+ * @param vMapListTo
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMapListTo(
+ final jalview.schemabinding.version2.MapListTo vMapListTo)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._mapListToList.addElement(vMapListTo);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMapListTo
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMapListTo(final int index,
+ final jalview.schemabinding.version2.MapListTo vMapListTo)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._mapListToList.add(index, vMapListTo);
+ }
+
+ /**
+ */
+ public void deleteMapFromUnit()
+ {
+ this._has_mapFromUnit = false;
+ }
+
+ /**
+ */
+ public void deleteMapToUnit()
+ {
+ this._has_mapToUnit = false;
+ }
+
+ /**
+ * Method enumerateMapListFrom.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom
+ * elements
+ */
+ public java.util.Enumeration enumerateMapListFrom()
+ {
+ return this._mapListFromList.elements();
+ }
+
+ /**
+ * Method enumerateMapListTo.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.MapListTo
+ * elements
+ */
+ public java.util.Enumeration enumerateMapListTo()
+ {
+ return this._mapListToList.elements();
+ }
+
+ /**
+ * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+ * following description: number of dictionary symbol widths involved in each
+ * mapped position on this sequence (for example, 3 for a dna sequence exon
+ * region that is being mapped to a protein sequence). This is optional, since
+ * the unit can be usually be inferred from the dictionary type of each
+ * sequence involved in the mapping.
+ *
+ * @return the value of field 'MapFromUnit'.
+ */
+ public long getMapFromUnit()
+ {
+ return this._mapFromUnit;
+ }
+
+ /**
+ * Method getMapListFrom.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.MapListFrom at the
+ * given index
+ */
+ public jalview.schemabinding.version2.MapListFrom getMapListFrom(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._mapListFromList.size())
+ {
+ throw new IndexOutOfBoundsException("getMapListFrom: Index value '"
+ + index + "' not in range [0.."
+ + (this._mapListFromList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.MapListFrom) _mapListFromList
+ .get(index);
+ }
+
+ /**
+ * Method getMapListFrom.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.MapListFrom[] getMapListFrom()
+ {
+ jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
+ return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList
+ .toArray(array);
+ }
+
+ /**
+ * Method getMapListFromCount.
+ *
+ * @return the size of this collection
+ */
+ public int getMapListFromCount()
+ {
+ return this._mapListFromList.size();
+ }
+
+ /**
+ * Method getMapListTo.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.MapListTo at the
+ * given index
+ */
+ public jalview.schemabinding.version2.MapListTo getMapListTo(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._mapListToList.size())
+ {
+ throw new IndexOutOfBoundsException("getMapListTo: Index value '"
+ + index + "' not in range [0.."
+ + (this._mapListToList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.MapListTo) _mapListToList
+ .get(index);
+ }
+
+ /**
+ * Method getMapListTo.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.MapListTo[] getMapListTo()
+ {
+ jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
+ return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList
+ .toArray(array);
+ }
+
+ /**
+ * Method getMapListToCount.
+ *
+ * @return the size of this collection
+ */
+ public int getMapListToCount()
+ {
+ return this._mapListToList.size();
+ }
+
+ /**
+ * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the
+ * following description: number of dictionary symbol widths involved in each
+ * mapped position on this sequence (for example, 3 for a dna sequence exon
+ * region that is being mapped to a protein sequence). This is optional, since
+ * the unit can be usually be inferred from the dictionary type of each
+ * sequence involved in the mapping.
+ *
+ * @return the value of field 'MapToUnit'.
+ */
+ public long getMapToUnit()
+ {
+ return this._mapToUnit;
+ }
+
+ /**
+ * Method hasMapFromUnit.
+ *
+ * @return true if at least one MapFromUnit has been added
+ */
+ public boolean hasMapFromUnit()
+ {
+ return this._has_mapFromUnit;
+ }
+
+ /**
+ * Method hasMapToUnit.
+ *
+ * @return true if at least one MapToUnit has been added
+ */
+ public boolean hasMapToUnit()
+ {
+ return this._has_mapToUnit;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllMapListFrom()
+ {
+ this._mapListFromList.clear();
+ }
+
+ /**
+ */
+ public void removeAllMapListTo()
+ {
+ this._mapListToList.clear();
+ }
+
+ /**
+ * Method removeMapListFrom.
+ *
+ * @param vMapListFrom
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeMapListFrom(
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+ {
+ boolean removed = _mapListFromList.remove(vMapListFrom);
+ return removed;
+ }
+
+ /**
+ * Method removeMapListFromAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
+ final int index)
+ {
+ java.lang.Object obj = this._mapListFromList.remove(index);
+ return (jalview.schemabinding.version2.MapListFrom) obj;
+ }
+
+ /**
+ * Method removeMapListTo.
+ *
+ * @param vMapListTo
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeMapListTo(
+ final jalview.schemabinding.version2.MapListTo vMapListTo)
+ {
+ boolean removed = _mapListToList.remove(vMapListTo);
+ return removed;
+ }
+
+ /**
+ * Method removeMapListToAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.MapListTo removeMapListToAt(
+ final int index)
+ {
+ java.lang.Object obj = this._mapListToList.remove(index);
+ return (jalview.schemabinding.version2.MapListTo) obj;
+ }
+
+ /**
+ * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+ * following description: number of dictionary symbol widths involved in each
+ * mapped position on this sequence (for example, 3 for a dna sequence exon
+ * region that is being mapped to a protein sequence). This is optional, since
+ * the unit can be usually be inferred from the dictionary type of each
+ * sequence involved in the mapping.
+ *
+ * @param mapFromUnit
+ * the value of field 'mapFromUnit'.
+ */
+ public void setMapFromUnit(final long mapFromUnit)
+ {
+ this._mapFromUnit = mapFromUnit;
+ this._has_mapFromUnit = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMapListFrom
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setMapListFrom(final int index,
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._mapListFromList.size())
+ {
+ throw new IndexOutOfBoundsException("setMapListFrom: Index value '"
+ + index + "' not in range [0.."
+ + (this._mapListFromList.size() - 1) + "]");
+ }
+
+ this._mapListFromList.set(index, vMapListFrom);
+ }
+
+ /**
+ *
+ *
+ * @param vMapListFromArray
+ */
+ public void setMapListFrom(
+ final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray)
+ {
+ // -- copy array
+ _mapListFromList.clear();
+
+ for (int i = 0; i < vMapListFromArray.length; i++)
+ {
+ this._mapListFromList.add(vMapListFromArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMapListTo
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setMapListTo(final int index,
+ final jalview.schemabinding.version2.MapListTo vMapListTo)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._mapListToList.size())
+ {
+ throw new IndexOutOfBoundsException("setMapListTo: Index value '"
+ + index + "' not in range [0.."
+ + (this._mapListToList.size() - 1) + "]");
+ }
+
+ this._mapListToList.set(index, vMapListTo);
+ }
+
+ /**
+ *
+ *
+ * @param vMapListToArray
+ */
+ public void setMapListTo(
+ final jalview.schemabinding.version2.MapListTo[] vMapListToArray)
+ {
+ // -- copy array
+ _mapListToList.clear();
+
+ for (int i = 0; i < vMapListToArray.length; i++)
+ {
+ this._mapListToList.add(vMapListToArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the
+ * following description: number of dictionary symbol widths involved in each
+ * mapped position on this sequence (for example, 3 for a dna sequence exon
+ * region that is being mapped to a protein sequence). This is optional, since
+ * the unit can be usually be inferred from the dictionary type of each
+ * sequence involved in the mapping.
+ *
+ * @param mapToUnit
+ * the value of field 'mapToUnit'.
+ */
+ public void setMapToUnit(final long mapToUnit)
+ {
+ this._mapToUnit = mapToUnit;
+ this._has_mapToUnit = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.MapListType
+ */
+ public static jalview.schemabinding.version2.MapListType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.MapListType.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Mapping extends jalview.schemabinding.version2.MapListType
-implements java.io.Serializable
+public class Mapping extends jalview.schemabinding.version2.MapListType
+ implements java.io.Serializable
{
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Internal choice value storage
- */
- private java.lang.Object _choiceValue;
-
- /**
- * Field _mappingChoice.
- */
- private jalview.schemabinding.version2.MappingChoice _mappingChoice;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Mapping() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'choiceValue'. The field
- * 'choiceValue' has the following description: Internal choice
- * value storage
- *
- * @return the value of field 'ChoiceValue'.
- */
- public java.lang.Object getChoiceValue(
- ) {
- return this._choiceValue;
- }
-
- /**
- * Returns the value of field 'mappingChoice'.
- *
- * @return the value of field 'MappingChoice'.
- */
- public jalview.schemabinding.version2.MappingChoice getMappingChoice(
- ) {
- return this._mappingChoice;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'mappingChoice'.
- *
- * @param mappingChoice the value of field 'mappingChoice'.
- */
- public void setMappingChoice(
- final jalview.schemabinding.version2.MappingChoice mappingChoice) {
- this._mappingChoice = mappingChoice;
- this._choiceValue = mappingChoice;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.MapListType
- */
- public static jalview.schemabinding.version2.MapListType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Internal choice value storage
+ */
+ private java.lang.Object _choiceValue;
+
+ /**
+ * Field _mappingChoice.
+ */
+ private jalview.schemabinding.version2.MappingChoice _mappingChoice;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Mapping()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+ * following description: Internal choice value storage
+ *
+ * @return the value of field 'ChoiceValue'.
+ */
+ public java.lang.Object getChoiceValue()
+ {
+ return this._choiceValue;
+ }
+
+ /**
+ * Returns the value of field 'mappingChoice'.
+ *
+ * @return the value of field 'MappingChoice'.
+ */
+ public jalview.schemabinding.version2.MappingChoice getMappingChoice()
+ {
+ return this._mappingChoice;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'mappingChoice'.
+ *
+ * @param mappingChoice
+ * the value of field 'mappingChoice'.
+ */
+ public void setMappingChoice(
+ final jalview.schemabinding.version2.MappingChoice mappingChoice)
+ {
+ this._mappingChoice = mappingChoice;
+ this._choiceValue = mappingChoice;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.MapListType
+ */
+ public static jalview.schemabinding.version2.MapListType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class MappingChoice implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _sequence.
- */
- private jalview.schemabinding.version2.Sequence _sequence;
-
- /**
- * Field _dseqFor.
- */
- private java.lang.String _dseqFor;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MappingChoice() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'dseqFor'.
- *
- * @return the value of field 'DseqFor'.
- */
- public java.lang.String getDseqFor(
- ) {
- return this._dseqFor;
- }
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public jalview.schemabinding.version2.Sequence getSequence(
- ) {
- return this._sequence;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'dseqFor'.
- *
- * @param dseqFor the value of field 'dseqFor'.
- */
- public void setDseqFor(
- final java.lang.String dseqFor) {
- this._dseqFor = dseqFor;
- }
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(
- final jalview.schemabinding.version2.Sequence sequence) {
- this._sequence = sequence;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.MappingChoice
- */
- public static jalview.schemabinding.version2.MappingChoice unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class MappingChoice implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _sequence.
+ */
+ private jalview.schemabinding.version2.Sequence _sequence;
+
+ /**
+ * Field _dseqFor.
+ */
+ private java.lang.String _dseqFor;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MappingChoice()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'dseqFor'.
+ *
+ * @return the value of field 'DseqFor'.
+ */
+ public java.lang.String getDseqFor()
+ {
+ return this._dseqFor;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public jalview.schemabinding.version2.Sequence getSequence()
+ {
+ return this._sequence;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'dseqFor'.
+ *
+ * @param dseqFor
+ * the value of field 'dseqFor'.
+ */
+ public void setDseqFor(final java.lang.String dseqFor)
+ {
+ this._dseqFor = dseqFor;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence
+ * the value of field 'sequence'.
+ */
+ public void setSequence(
+ final jalview.schemabinding.version2.Sequence sequence)
+ {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.MappingChoice
+ */
+ public static jalview.schemabinding.version2.MappingChoice unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.MappingChoice) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.MappingChoice.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class OtherData implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _key.
- */
- private java.lang.String _key;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public OtherData() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'key'.
- *
- * @return the value of field 'Key'.
- */
- public java.lang.String getKey(
- ) {
- return this._key;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'key'.
- *
- * @param key the value of field 'key'.
- */
- public void setKey(
- final java.lang.String key) {
- this._key = key;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final java.lang.String value) {
- this._value = value;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.OtherData
- */
- public static jalview.schemabinding.version2.OtherData unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class OtherData implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _key.
+ */
+ private java.lang.String _key;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public OtherData()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'key'.
+ *
+ * @return the value of field 'Key'.
+ */
+ public java.lang.String getKey()
+ {
+ return this._key;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'key'.
+ *
+ * @param key
+ * the value of field 'key'.
+ */
+ public void setKey(final java.lang.String key)
+ {
+ this._key = key;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final java.lang.String value)
+ {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.OtherData
+ */
+ public static jalview.schemabinding.version2.OtherData unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.OtherData) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.OtherData.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbentry implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _file.
- */
- private java.lang.String _file;
-
- /**
- * Field _items.
- */
- private java.util.Vector _items;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Pdbentry() {
- super();
- this._items = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- this._items.addElement(vPdbentryItem);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final int index,
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- this._items.add(index, vPdbentryItem);
- }
-
- /**
- * Method enumeratePdbentryItem.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.PdbentryItem elements
- */
- public java.util.Enumeration enumeratePdbentryItem(
- ) {
- return this._items.elements();
- }
-
- /**
- * Returns the value of field 'file'.
- *
- * @return the value of field 'File'.
- */
- public java.lang.String getFile(
- ) {
- return this._file;
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Method getPdbentryItem.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.PdbentryItem at the given inde
- */
- public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._items.size()) {
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
- }
-
- /**
- * Method getPdbentryItem.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem(
- ) {
- jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
- return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array);
- }
-
- /**
- * Method getPdbentryItemCount.
- *
- * @return the size of this collection
- */
- public int getPdbentryItemCount(
- ) {
- return this._items.size();
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllPdbentryItem(
- ) {
- this._items.clear();
- }
-
- /**
- * Method removePdbentryItem.
- *
- * @param vPdbentryItem
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbentryItem(
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) {
- boolean removed = _items.remove(vPdbentryItem);
- return removed;
- }
-
- /**
- * Method removePdbentryItemAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
- final int index) {
- java.lang.Object obj = this._items.remove(index);
- return (jalview.schemabinding.version2.PdbentryItem) obj;
- }
-
- /**
- * Sets the value of field 'file'.
- *
- * @param file the value of field 'file'.
- */
- public void setFile(
- final java.lang.String file) {
- this._file = file;
+public class Pdbentry implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _file.
+ */
+ private java.lang.String _file;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Pdbentry()
+ {
+ super();
+ this._items = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(final int index,
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem()
+ {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'file'.
+ *
+ * @return the value of field 'File'.
+ */
+ public java.lang.String getFile()
+ {
+ return this._file;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.PdbentryItem at the
+ * given inde
+ */
+ public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size())
+ {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+ + index + "' not in range [0.." + (this._items.size() - 1)
+ + "]");
}
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
+ return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+ {
+ jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
+ return (jalview.schemabinding.version2.PdbentryItem[]) this._items
+ .toArray(array);
+ }
+
+ /**
+ * Method getPdbentryItemCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbentryItemCount()
+ {
+ return this._items.size();
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setPdbentryItem(
- final int index,
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._items.size()) {
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
- }
-
- this._items.set(index, vPdbentryItem);
+ public void removeAllPdbentryItem()
+ {
+ this._items.clear();
+ }
+
+ /**
+ * Method removePdbentryItem.
+ *
+ * @param vPdbentryItem
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbentryItem(
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
+ final int index)
+ {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.schemabinding.version2.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'file'.
+ *
+ * @param file
+ * the value of field 'file'.
+ */
+ public void setFile(final java.lang.String file)
+ {
+ this._file = file;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPdbentryItem(final int index,
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size())
+ {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+ + index + "' not in range [0.." + (this._items.size() - 1)
+ + "]");
}
- /**
- *
- *
- * @param vPdbentryItemArray
- */
- public void setPdbentryItem(
- final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) {
- //-- copy array
- _items.clear();
-
- for (int i = 0; i < vPdbentryItemArray.length; i++) {
- this._items.add(vPdbentryItemArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Pdbentry
- */
- public static jalview.schemabinding.version2.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)
+ {
+ // -- copy array
+ _items.clear();
+
+ for (int i = 0; i < vPdbentryItemArray.length; i++)
+ {
+ this._items.add(vPdbentryItemArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+ */
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Pdbentry.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
*
* @version $Revision$ $Date$
*/
-public class PdbentryItem implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PdbentryItem() {
- super();
- this._propertyList = new java.util.Vector();
+public class PdbentryItem implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PdbentryItem()
+ {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Property
+ * elements
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Property at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ return (jalview.schemabinding.version2.Property) _propertyList
+ .get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Property[] getProperty()
+ {
+ jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+ return (jalview.schemabinding.version2.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount()
+ {
+ return this._propertyList.size();
+ }
+
+ /**
*/
- public void addProperty(
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
+ public void removeAllProperty()
+ {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.schemabinding.version2.Property vProperty)
+ {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Property removePropertyAt(
+ final int index)
+ {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.schemabinding.version2.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size())
+ {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"
+ + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.elements();
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Property at the given index
- */
- public jalview.schemabinding.version2.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Property[] getProperty(
- ) {
- jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
- return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final jalview.schemabinding.version2.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (jalview.schemabinding.version2.Property) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final jalview.schemabinding.version2.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final jalview.schemabinding.version2.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
- }
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.schemabinding.version2.Property[] vPropertyArray)
+ {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++)
+ {
+ this._propertyList.add(vPropertyArray[i]);
}
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry
-implements java.io.Serializable
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+ implements java.io.Serializable
{
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * Field _structureStateList.
+ */
+ private java.util.Vector _structureStateList;
- /**
- * Field _structureStateList.
- */
- private java.util.Vector _structureStateList;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public Pdbids()
+ {
+ super();
+ this._structureStateList = new java.util.Vector();
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public Pdbids() {
- super();
- this._structureStateList = new java.util.Vector();
- }
+ /**
+ *
+ *
+ * @param vStructureState
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addStructureState(
+ final jalview.schemabinding.version2.StructureState vStructureState)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._structureStateList.addElement(vStructureState);
+ }
+ /**
+ *
+ *
+ * @param index
+ * @param vStructureState
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addStructureState(
+ final int index,
+ final jalview.schemabinding.version2.StructureState vStructureState)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._structureStateList.add(index, vStructureState);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ * Method enumerateStructureState.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.StructureState elements
+ */
+ public java.util.Enumeration enumerateStructureState()
+ {
+ return this._structureStateList.elements();
+ }
- /**
- *
- *
- * @param vStructureState
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addStructureState(
- final jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException {
- this._structureStateList.addElement(vStructureState);
+ /**
+ * Method getStructureState.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.StructureState at
+ * the given index
+ */
+ public jalview.schemabinding.version2.StructureState getStructureState(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._structureStateList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getStructureState: Index value '" + index
+ + "' not in range [0.."
+ + (this._structureStateList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vStructureState
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addStructureState(
- final int index,
- final jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException {
- this._structureStateList.add(index, vStructureState);
- }
+ return (jalview.schemabinding.version2.StructureState) _structureStateList
+ .get(index);
+ }
- /**
- * Method enumerateStructureState.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.StructureState elements
- */
- public java.util.Enumeration enumerateStructureState(
- ) {
- return this._structureStateList.elements();
- }
+ /**
+ * Method getStructureState.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.StructureState[] getStructureState()
+ {
+ jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
+ return (jalview.schemabinding.version2.StructureState[]) this._structureStateList
+ .toArray(array);
+ }
- /**
- * Method getStructureState.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.StructureState at the given
- * index
- */
- public jalview.schemabinding.version2.StructureState getStructureState(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._structureStateList.size()) {
- throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);
- }
+ /**
+ * Method getStructureStateCount.
+ *
+ * @return the size of this collection
+ */
+ public int getStructureStateCount()
+ {
+ return this._structureStateList.size();
+ }
- /**
- * Method getStructureState.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.StructureState[] getStructureState(
- ) {
- jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
- return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array);
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- * Method getStructureStateCount.
- *
- * @return the size of this collection
- */
- public int getStructureStateCount(
- ) {
- return this._structureStateList.size();
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+ /**
*/
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ public void removeAllStructureState()
+ {
+ this._structureStateList.clear();
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ * Method removeStructureState.
+ *
+ * @param vStructureState
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeStructureState(
+ final jalview.schemabinding.version2.StructureState vStructureState)
+ {
+ boolean removed = _structureStateList.remove(vStructureState);
+ return removed;
+ }
- /**
- */
- public void removeAllStructureState(
- ) {
- this._structureStateList.clear();
- }
+ /**
+ * Method removeStructureStateAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.StructureState removeStructureStateAt(
+ final int index)
+ {
+ java.lang.Object obj = this._structureStateList.remove(index);
+ return (jalview.schemabinding.version2.StructureState) obj;
+ }
- /**
- * Method removeStructureState.
- *
- * @param vStructureState
- * @return true if the object was removed from the collection.
- */
- public boolean removeStructureState(
- final jalview.schemabinding.version2.StructureState vStructureState) {
- boolean removed = _structureStateList.remove(vStructureState);
- return removed;
+ /**
+ *
+ *
+ * @param index
+ * @param vStructureState
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setStructureState(
+ final int index,
+ final jalview.schemabinding.version2.StructureState vStructureState)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._structureStateList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setStructureState: Index value '" + index
+ + "' not in range [0.."
+ + (this._structureStateList.size() - 1) + "]");
}
- /**
- * Method removeStructureStateAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.StructureState removeStructureStateAt(
- final int index) {
- java.lang.Object obj = this._structureStateList.remove(index);
- return (jalview.schemabinding.version2.StructureState) obj;
- }
+ this._structureStateList.set(index, vStructureState);
+ }
- /**
- *
- *
- * @param index
- * @param vStructureState
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setStructureState(
- final int index,
- final jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._structureStateList.size()) {
- throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
- }
-
- this._structureStateList.set(index, vStructureState);
- }
+ /**
+ *
+ *
+ * @param vStructureStateArray
+ */
+ public void setStructureState(
+ final jalview.schemabinding.version2.StructureState[] vStructureStateArray)
+ {
+ // -- copy array
+ _structureStateList.clear();
- /**
- *
- *
- * @param vStructureStateArray
- */
- public void setStructureState(
- final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {
- //-- copy array
- _structureStateList.clear();
-
- for (int i = 0; i < vStructureStateArray.length; i++) {
- this._structureStateList.add(vStructureStateArray[i]);
- }
+ for (int i = 0; i < vStructureStateArray.length; i++)
+ {
+ this._structureStateList.add(vStructureStateArray[i]);
}
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Pdbentry
- */
- public static jalview.schemabinding.version2.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+ */
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Property implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Property() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final java.lang.String value) {
- this._value = value;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Property
- */
- public static jalview.schemabinding.version2.Property unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Property()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final java.lang.String value)
+ {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Property
+ */
+ public static jalview.schemabinding.version2.Property unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Property) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Property.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
/**
- * Reference to a viewer showing RNA structure
- * for this sequence. Schema supports one viewer showing multiple
- * annotations for multiple sequences, though currently only one
- * annotation for one sequence (gapped or trimmed) is used
- *
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed) is
+ * used
+ *
*
* @version $Revision$ $Date$
*/
-public class RnaViewer implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * An id unique to the RNA viewer panel
- *
- */
- private java.lang.String _viewId;
-
- /**
- * horizontal position of split pane divider
- *
- */
- private int _dividerLocation;
-
- /**
- * keeps track of state for field: _dividerLocation
- */
- private boolean _has_dividerLocation;
-
- /**
- * Index of the selected structure in the
- * viewer panel
- *
- */
- private int _selectedRna;
-
- /**
- * keeps track of state for field: _selectedRna
- */
- private boolean _has_selectedRna;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _secondaryStructureList.
- */
- private java.util.Vector _secondaryStructureList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public RnaViewer() {
- super();
- this._secondaryStructureList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSecondaryStructure
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSecondaryStructure(
- final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
- throws java.lang.IndexOutOfBoundsException {
- this._secondaryStructureList.addElement(vSecondaryStructure);
- }
-
- /**
- *
- *
- * @param index
- * @param vSecondaryStructure
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSecondaryStructure(
- final int index,
- final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
- throws java.lang.IndexOutOfBoundsException {
- this._secondaryStructureList.add(index, vSecondaryStructure);
- }
-
- /**
- */
- public void deleteDividerLocation(
- ) {
- this._has_dividerLocation= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteSelectedRna(
- ) {
- this._has_selectedRna= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Method enumerateSecondaryStructure.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.SecondaryStructure elements
- */
- public java.util.Enumeration enumerateSecondaryStructure(
- ) {
- return this._secondaryStructureList.elements();
- }
-
- /**
- * Returns the value of field 'dividerLocation'. The field
- * 'dividerLocation' has the following description: horizontal
- * position of split pane divider
- *
- *
- * @return the value of field 'DividerLocation'.
- */
- public int getDividerLocation(
- ) {
- return this._dividerLocation;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Method getSecondaryStructure.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.SecondaryStructure at the
- * given index
- */
- public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._secondaryStructureList.size()) {
- throw new IndexOutOfBoundsException("getSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList.get(index);
- }
-
- /**
- * Method getSecondaryStructure.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure(
- ) {
- jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
- return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList.toArray(array);
- }
-
- /**
- * Method getSecondaryStructureCount.
- *
- * @return the size of this collection
- */
- public int getSecondaryStructureCount(
- ) {
- return this._secondaryStructureList.size();
- }
-
- /**
- * Returns the value of field 'selectedRna'. The field
- * 'selectedRna' has the following description: Index of the
- * selected structure in the
- * viewer panel
- *
- *
- * @return the value of field 'SelectedRna'.
- */
- public int getSelectedRna(
- ) {
- return this._selectedRna;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewId'. The field 'viewId' has
- * the following description: An id unique to the RNA viewer
- * panel
- *
- *
- * @return the value of field 'ViewId'.
- */
- public java.lang.String getViewId(
- ) {
- return this._viewId;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasDividerLocation.
- *
- * @return true if at least one DividerLocation has been added
- */
- public boolean hasDividerLocation(
- ) {
- return this._has_dividerLocation;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasSelectedRna.
- *
- * @return true if at least one SelectedRna has been added
- */
- public boolean hasSelectedRna(
- ) {
- return this._has_selectedRna;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllSecondaryStructure(
- ) {
- this._secondaryStructureList.clear();
- }
-
- /**
- * Method removeSecondaryStructure.
- *
- * @param vSecondaryStructure
- * @return true if the object was removed from the collection.
- */
- public boolean removeSecondaryStructure(
- final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) {
- boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
- return removed;
- }
-
- /**
- * Method removeSecondaryStructureAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
- final int index) {
- java.lang.Object obj = this._secondaryStructureList.remove(index);
- return (jalview.schemabinding.version2.SecondaryStructure) obj;
- }
-
- /**
- * Sets the value of field 'dividerLocation'. The field
- * 'dividerLocation' has the following description: horizontal
- * position of split pane divider
- *
- *
- * @param dividerLocation the value of field 'dividerLocation'.
- */
- public void setDividerLocation(
- final int dividerLocation) {
- this._dividerLocation = dividerLocation;
- this._has_dividerLocation = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSecondaryStructure
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSecondaryStructure(
- final int index,
- final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._secondaryStructureList.size()) {
- throw new IndexOutOfBoundsException("setSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
- }
-
- this._secondaryStructureList.set(index, vSecondaryStructure);
- }
-
- /**
- *
- *
- * @param vSecondaryStructureArray
- */
- public void setSecondaryStructure(
- final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray) {
- //-- copy array
- _secondaryStructureList.clear();
-
- for (int i = 0; i < vSecondaryStructureArray.length; i++) {
- this._secondaryStructureList.add(vSecondaryStructureArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'selectedRna'. The field
- * 'selectedRna' has the following description: Index of the
- * selected structure in the
- * viewer panel
- *
- *
- * @param selectedRna the value of field 'selectedRna'.
- */
- public void setSelectedRna(
- final int selectedRna) {
- this._selectedRna = selectedRna;
- this._has_selectedRna = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewId'. The field 'viewId' has the
- * following description: An id unique to the RNA viewer panel
- *
- *
- * @param viewId the value of field 'viewId'.
- */
- public void setViewId(
- final java.lang.String viewId) {
- this._viewId = viewId;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.RnaViewer
- */
- public static jalview.schemabinding.version2.RnaViewer unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.RnaViewer) Unmarshaller.unmarshal(jalview.schemabinding.version2.RnaViewer.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class RnaViewer implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * An id unique to the RNA viewer panel
+ *
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * horizontal position of split pane divider
+ *
+ */
+ private int _dividerLocation;
+
+ /**
+ * keeps track of state for field: _dividerLocation
+ */
+ private boolean _has_dividerLocation;
+
+ /**
+ * Index of the selected structure in the viewer panel
+ *
+ */
+ private int _selectedRna;
+
+ /**
+ * keeps track of state for field: _selectedRna
+ */
+ private boolean _has_selectedRna;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _secondaryStructureList.
+ */
+ private java.util.Vector _secondaryStructureList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public RnaViewer()
+ {
+ super();
+ this._secondaryStructureList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._secondaryStructureList.addElement(vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._secondaryStructureList.add(index, vSecondaryStructure);
+ }
+
+ /**
+ */
+ public void deleteDividerLocation()
+ {
+ this._has_dividerLocation = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteSelectedRna()
+ {
+ this._has_selectedRna = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Method enumerateSecondaryStructure.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SecondaryStructure elements
+ */
+ public java.util.Enumeration enumerateSecondaryStructure()
+ {
+ return this._secondaryStructureList.elements();
+ }
+
+ /**
+ * Returns the value of field 'dividerLocation'. The field 'dividerLocation'
+ * has the following description: horizontal position of split pane divider
+ *
+ *
+ * @return the value of field 'DividerLocation'.
+ */
+ public int getDividerLocation()
+ {
+ return this._dividerLocation;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Method getSecondaryStructure.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.SecondaryStructure
+ * at the given index
+ */
+ public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getSecondaryStructure: Index value '" + index
+ + "' not in range [0.."
+ + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList
+ .get(index);
+ }
+
+ /**
+ * Method getSecondaryStructure.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure()
+ {
+ jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
+ return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSecondaryStructureCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSecondaryStructureCount()
+ {
+ return this._secondaryStructureList.size();
+ }
+
+ /**
+ * Returns the value of field 'selectedRna'. The field 'selectedRna' has the
+ * following description: Index of the selected structure in the viewer panel
+ *
+ *
+ * @return the value of field 'SelectedRna'.
+ */
+ public int getSelectedRna()
+ {
+ return this._selectedRna;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewId'. The field 'viewId' has the following
+ * description: An id unique to the RNA viewer panel
+ *
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId()
+ {
+ return this._viewId;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasDividerLocation.
+ *
+ * @return true if at least one DividerLocation has been added
+ */
+ public boolean hasDividerLocation()
+ {
+ return this._has_dividerLocation;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasSelectedRna.
+ *
+ * @return true if at least one SelectedRna has been added
+ */
+ public boolean hasSelectedRna()
+ {
+ return this._has_selectedRna;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSecondaryStructure()
+ {
+ this._secondaryStructureList.clear();
+ }
+
+ /**
+ * Method removeSecondaryStructure.
+ *
+ * @param vSecondaryStructure
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ {
+ boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
+ return removed;
+ }
+
+ /**
+ * Method removeSecondaryStructureAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
+ final int index)
+ {
+ java.lang.Object obj = this._secondaryStructureList.remove(index);
+ return (jalview.schemabinding.version2.SecondaryStructure) obj;
+ }
+
+ /**
+ * Sets the value of field 'dividerLocation'. The field 'dividerLocation' has
+ * the following description: horizontal position of split pane divider
+ *
+ *
+ * @param dividerLocation
+ * the value of field 'dividerLocation'.
+ */
+ public void setDividerLocation(final int dividerLocation)
+ {
+ this._dividerLocation = dividerLocation;
+ this._has_dividerLocation = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setSecondaryStructure: Index value '" + index
+ + "' not in range [0.."
+ + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ this._secondaryStructureList.set(index, vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param vSecondaryStructureArray
+ */
+ public void setSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray)
+ {
+ // -- copy array
+ _secondaryStructureList.clear();
+
+ for (int i = 0; i < vSecondaryStructureArray.length; i++)
+ {
+ this._secondaryStructureList.add(vSecondaryStructureArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'selectedRna'. The field 'selectedRna' has the
+ * following description: Index of the selected structure in the viewer panel
+ *
+ *
+ * @param selectedRna
+ * the value of field 'selectedRna'.
+ */
+ public void setSelectedRna(final int selectedRna)
+ {
+ this._selectedRna = selectedRna;
+ this._has_selectedRna = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewId'. The field 'viewId' has the following
+ * description: An id unique to the RNA viewer panel
+ *
+ *
+ * @param viewId
+ * the value of field 'viewId'.
+ */
+ public void setViewId(final java.lang.String viewId)
+ {
+ this._viewId = viewId;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.RnaViewer
+ */
+ public static jalview.schemabinding.version2.RnaViewer unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.RnaViewer) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.RnaViewer.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SecondaryStructure implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * id attribute of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- */
- private java.lang.String _annotationId;
-
- /**
- * if true the RNA structure is shown with gaps, if false
- * without
- *
- */
- private boolean _gapped;
-
- /**
- * keeps track of state for field: _gapped
- */
- private boolean _has_gapped;
-
- /**
- * name of the project jar entry that holds
- * the VARNA viewer state for the structure
- *
- */
- private java.lang.String _viewerState;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SecondaryStructure() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteGapped(
- ) {
- this._has_gapped= false;
- }
-
- /**
- * Returns the value of field 'annotationId'. The field
- * 'annotationId' has the following description: id attribute
- * of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- *
- * @return the value of field 'AnnotationId'.
- */
- public java.lang.String getAnnotationId(
- ) {
- return this._annotationId;
- }
-
- /**
- * Returns the value of field 'gapped'. The field 'gapped' has
- * the following description: if true the RNA structure is
- * shown with gaps, if false without
- *
- *
- * @return the value of field 'Gapped'.
- */
- public boolean getGapped(
- ) {
- return this._gapped;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewerState'. The field
- * 'viewerState' has the following description: name of the
- * project jar entry that holds
- * the VARNA viewer state for the structure
- *
- *
- * @return the value of field 'ViewerState'.
- */
- public java.lang.String getViewerState(
- ) {
- return this._viewerState;
- }
-
- /**
- * Method hasGapped.
- *
- * @return true if at least one Gapped has been added
- */
- public boolean hasGapped(
- ) {
- return this._has_gapped;
- }
-
- /**
- * Returns the value of field 'gapped'. The field 'gapped' has
- * the following description: if true the RNA structure is
- * shown with gaps, if false without
- *
- *
- * @return the value of field 'Gapped'.
- */
- public boolean isGapped(
- ) {
- return this._gapped;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'annotationId'. The field
- * 'annotationId' has the following description: id attribute
- * of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- *
- * @param annotationId the value of field 'annotationId'.
- */
- public void setAnnotationId(
- final java.lang.String annotationId) {
- this._annotationId = annotationId;
- }
-
- /**
- * Sets the value of field 'gapped'. The field 'gapped' has the
- * following description: if true the RNA structure is shown
- * with gaps, if false without
- *
- *
- * @param gapped the value of field 'gapped'.
- */
- public void setGapped(
- final boolean gapped) {
- this._gapped = gapped;
- this._has_gapped = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewerState'. The field
- * 'viewerState' has the following description: name of the
- * project jar entry that holds
- * the VARNA viewer state for the structure
- *
- *
- * @param viewerState the value of field 'viewerState'.
- */
- public void setViewerState(
- final java.lang.String viewerState) {
- this._viewerState = viewerState;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SecondaryStructure
- */
- public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
+public class SecondaryStructure implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * id attribute of Annotation in vamsasModel for the secondary structure
+ * annotation shown in the viewer
+ *
+ */
+ private java.lang.String _annotationId;
+
+ /**
+ * if true the RNA structure is shown with gaps, if false without
+ *
+ */
+ private boolean _gapped;
+
+ /**
+ * keeps track of state for field: _gapped
+ */
+ private boolean _has_gapped;
+
+ /**
+ * name of the project jar entry that holds the VARNA viewer state for the
+ * structure
+ *
+ */
+ private java.lang.String _viewerState;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SecondaryStructure()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
*/
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ public void deleteGapped()
+ {
+ this._has_gapped = false;
+ }
+
+ /**
+ * Returns the value of field 'annotationId'. The field 'annotationId' has the
+ * following description: id attribute of Annotation in vamsasModel for the
+ * secondary structure annotation shown in the viewer
+ *
+ *
+ * @return the value of field 'AnnotationId'.
+ */
+ public java.lang.String getAnnotationId()
+ {
+ return this._annotationId;
+ }
+
+ /**
+ * Returns the value of field 'gapped'. The field 'gapped' has the following
+ * description: if true the RNA structure is shown with gaps, if false without
+ *
+ *
+ * @return the value of field 'Gapped'.
+ */
+ public boolean getGapped()
+ {
+ return this._gapped;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewerState'. The field 'viewerState' has the
+ * following description: name of the project jar entry that holds the VARNA
+ * viewer state for the structure
+ *
+ *
+ * @return the value of field 'ViewerState'.
+ */
+ public java.lang.String getViewerState()
+ {
+ return this._viewerState;
+ }
+
+ /**
+ * Method hasGapped.
+ *
+ * @return true if at least one Gapped has been added
+ */
+ public boolean hasGapped()
+ {
+ return this._has_gapped;
+ }
+
+ /**
+ * Returns the value of field 'gapped'. The field 'gapped' has the following
+ * description: if true the RNA structure is shown with gaps, if false without
+ *
+ *
+ * @return the value of field 'Gapped'.
+ */
+ public boolean isGapped()
+ {
+ return this._gapped;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'annotationId'. The field 'annotationId' has the
+ * following description: id attribute of Annotation in vamsasModel for the
+ * secondary structure annotation shown in the viewer
+ *
+ *
+ * @param annotationId
+ * the value of field 'annotationId'.
+ */
+ public void setAnnotationId(final java.lang.String annotationId)
+ {
+ this._annotationId = annotationId;
+ }
+
+ /**
+ * Sets the value of field 'gapped'. The field 'gapped' has the following
+ * description: if true the RNA structure is shown with gaps, if false without
+ *
+ *
+ * @param gapped
+ * the value of field 'gapped'.
+ */
+ public void setGapped(final boolean gapped)
+ {
+ this._gapped = gapped;
+ this._has_gapped = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewerState'. The field 'viewerState' has the
+ * following description: name of the project jar entry that holds the VARNA
+ * viewer state for the structure
+ *
+ *
+ * @param viewerState
+ * the value of field 'viewerState'.
+ */
+ public void setViewerState(final java.lang.String viewerState)
+ {
+ this._viewerState = viewerState;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SecondaryStructure
+ */
+ public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.SecondaryStructure.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Sequence extends jalview.schemabinding.version2.SequenceType
-implements java.io.Serializable
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+ implements java.io.Serializable
{
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * dataset sequence id for this sequence. Will be created as
- * union of sequences.
- *
- */
- private java.lang.String _dsseqid;
-
- /**
- * Field _DBRefList.
- */
- private java.util.Vector _DBRefList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence() {
- super();
- this._DBRefList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDBRef(
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- this._DBRefList.addElement(vDBRef);
- }
-
- /**
- *
- *
- * @param index
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDBRef(
- final int index,
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- this._DBRefList.add(index, vDBRef);
- }
-
- /**
- * Method enumerateDBRef.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.DBRef elements
- */
- public java.util.Enumeration enumerateDBRef(
- ) {
- return this._DBRefList.elements();
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * dataset sequence id for this sequence. Will be created as union of
+ * sequences.
+ *
+ */
+ private java.lang.String _dsseqid;
+
+ /**
+ * Field _DBRefList.
+ */
+ private java.util.Vector _DBRefList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Sequence()
+ {
+ super();
+ this._DBRefList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.addElement(vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.add(index, vDBRef);
+ }
+
+ /**
+ * Method enumerateDBRef.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+ * elements
+ */
+ public java.util.Enumeration enumerateDBRef()
+ {
+ return this._DBRefList.elements();
+ }
+
+ /**
+ * Method getDBRef.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.DBRef at the given
+ * index
+ */
+ public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
}
- /**
- * Method getDBRef.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.DBRef at the given index
- */
- public jalview.schemabinding.version2.DBRef getDBRef(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._DBRefList.size()) {
- throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+ }
+
+ /**
+ * Method getDBRef.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.DBRef[] getDBRef()
+ {
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+ .toArray(array);
+ }
+
+ /**
+ * Method getDBRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDBRefCount()
+ {
+ return this._DBRefList.size();
+ }
+
+ /**
+ * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @return the value of field 'Dsseqid'.
+ */
+ public java.lang.String getDsseqid()
+ {
+ return this._dsseqid;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- * Method getDBRef.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public jalview.schemabinding.version2.DBRef[] getDBRef(
- ) {
- jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
- return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
+ public void removeAllDBRef()
+ {
+ this._DBRefList.clear();
+ }
+
+ /**
+ * Method removeDBRef.
+ *
+ * @param vDBRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDBRef(
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ {
+ boolean removed = _DBRefList.remove(vDBRef);
+ return removed;
+ }
+
+ /**
+ * Method removeDBRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+ {
+ java.lang.Object obj = this._DBRefList.remove(index);
+ return (jalview.schemabinding.version2.DBRef) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
}
- /**
- * Method getDBRefCount.
- *
- * @return the size of this collection
- */
- public int getDBRefCount(
- ) {
- return this._DBRefList.size();
- }
-
- /**
- * Returns the value of field 'dsseqid'. The field 'dsseqid'
- * has the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @return the value of field 'Dsseqid'.
- */
- public java.lang.String getDsseqid(
- ) {
- return this._dsseqid;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllDBRef(
- ) {
- this._DBRefList.clear();
- }
-
- /**
- * Method removeDBRef.
- *
- * @param vDBRef
- * @return true if the object was removed from the collection.
- */
- public boolean removeDBRef(
- final jalview.schemabinding.version2.DBRef vDBRef) {
- boolean removed = _DBRefList.remove(vDBRef);
- return removed;
- }
-
- /**
- * Method removeDBRefAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.DBRef removeDBRefAt(
- final int index) {
- java.lang.Object obj = this._DBRefList.remove(index);
- return (jalview.schemabinding.version2.DBRef) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setDBRef(
- final int index,
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._DBRefList.size()) {
- throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
- }
-
- this._DBRefList.set(index, vDBRef);
- }
-
- /**
- *
- *
- * @param vDBRefArray
- */
- public void setDBRef(
- final jalview.schemabinding.version2.DBRef[] vDBRefArray) {
- //-- copy array
- _DBRefList.clear();
-
- for (int i = 0; i < vDBRefArray.length; i++) {
- this._DBRefList.add(vDBRefArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'dsseqid'. The field 'dsseqid' has
- * the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @param dsseqid the value of field 'dsseqid'.
- */
- public void setDsseqid(
- final java.lang.String dsseqid) {
- this._dsseqid = dsseqid;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceType
- */
- public static jalview.schemabinding.version2.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._DBRefList.set(index, vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param vDBRefArray
+ */
+ public void setDBRef(
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+ {
+ // -- copy array
+ _DBRefList.clear();
+
+ for (int i = 0; i < vDBRefArray.length; i++)
+ {
+ this._DBRefList.add(vDBRefArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @param dsseqid
+ * the value of field 'dsseqid'.
+ */
+ public void setDsseqid(final java.lang.String dsseqid)
+ {
+ this._dsseqid = dsseqid;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+ */
+ public static jalview.schemabinding.version2.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Sequence.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSet implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _gapChar.
- */
- private java.lang.String _gapChar;
-
- /**
- * reference to set where jalview will gather the dataset
- * sequences for all sequences in the set.
- *
- */
- private java.lang.String _datasetId;
-
- /**
- * Field _sequenceList.
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList.
- */
- private java.util.Vector _annotationList;
-
- /**
- * Field _sequenceSetPropertiesList.
- */
- private java.util.Vector _sequenceSetPropertiesList;
-
- /**
- * Field _alcodonFrameList.
- */
- private java.util.Vector _alcodonFrameList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSet() {
- super();
- this._sequenceList = new java.util.Vector();
- this._annotationList = new java.util.Vector();
- this._sequenceSetPropertiesList = new java.util.Vector();
- this._alcodonFrameList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodonFrameList.addElement(vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlcodonFrame(
- final int index,
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException {
- this._alcodonFrameList.add(index, vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotation(
- final jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationList.addElement(vAnnotation);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAnnotation(
- final int index,
- final jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._annotationList.add(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequence(
- final jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceList.addElement(vSequence);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequence(
- final int index,
- final jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceList.add(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSetProperties(
- final int index,
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
- }
-
- /**
- * Method enumerateAlcodonFrame.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.AlcodonFrame elements
- */
- public java.util.Enumeration enumerateAlcodonFrame(
- ) {
- return this._alcodonFrameList.elements();
- }
-
- /**
- * Method enumerateAnnotation.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Annotation elements
- */
- public java.util.Enumeration enumerateAnnotation(
- ) {
- return this._annotationList.elements();
- }
-
- /**
- * Method enumerateSequence.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.Sequence elements
- */
- public java.util.Enumeration enumerateSequence(
- ) {
- return this._sequenceList.elements();
- }
-
- /**
- * Method enumerateSequenceSetProperties.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.SequenceSetProperties elements
- */
- public java.util.Enumeration enumerateSequenceSetProperties(
- ) {
- return this._sequenceSetPropertiesList.elements();
- }
-
- /**
- * Method getAlcodonFrame.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.AlcodonFrame at the given inde
- */
- public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodonFrameList.size()) {
- throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);
- }
-
- /**
- * Method getAlcodonFrame.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(
- ) {
- jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
- return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);
- }
-
- /**
- * Method getAlcodonFrameCount.
- *
- * @return the size of this collection
- */
- public int getAlcodonFrameCount(
- ) {
- return this._alcodonFrameList.size();
- }
-
- /**
- * Method getAnnotation.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Annotation at the given index
- */
- public jalview.schemabinding.version2.Annotation getAnnotation(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size()) {
- throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Annotation) _annotationList.get(index);
- }
-
- /**
- * Method getAnnotation.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Annotation[] getAnnotation(
- ) {
- jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
- return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array);
- }
-
- /**
- * Method getAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationCount(
- ) {
- return this._annotationList.size();
- }
-
- /**
- * Returns the value of field 'datasetId'. The field
- * 'datasetId' has the following description: reference to set
- * where jalview will gather the dataset sequences for all
- * sequences in the set.
- *
- *
- * @return the value of field 'DatasetId'.
- */
- public java.lang.String getDatasetId(
- ) {
- return this._datasetId;
- }
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return the value of field 'GapChar'.
- */
- public java.lang.String getGapChar(
- ) {
- return this._gapChar;
- }
-
- /**
- * Method getSequence.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.Sequence at the given index
- */
- public jalview.schemabinding.version2.Sequence getSequence(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size()) {
- throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index);
- }
-
- /**
- * Method getSequence.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.Sequence[] getSequence(
- ) {
- jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
- return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);
- }
-
- /**
- * Method getSequenceCount.
- *
- * @return the size of this collection
- */
- public int getSequenceCount(
- ) {
- return this._sequenceList.size();
- }
-
- /**
- * Method getSequenceSetProperties.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.SequenceSetProperties at the
- * given index
- */
- public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
- throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);
- }
-
- /**
- * Method getSequenceSetProperties.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(
- ) {
- jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
- return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);
- }
-
- /**
- * Method getSequenceSetPropertiesCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetPropertiesCount(
- ) {
- return this._sequenceSetPropertiesList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlcodonFrame.
- *
- * @param vAlcodonFrame
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
- boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
- return removed;
- }
-
- /**
- * Method removeAlcodonFrameAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
- final int index) {
- java.lang.Object obj = this._alcodonFrameList.remove(index);
- return (jalview.schemabinding.version2.AlcodonFrame) obj;
- }
-
- /**
- */
- public void removeAllAlcodonFrame(
- ) {
- this._alcodonFrameList.clear();
- }
-
- /**
- */
- public void removeAllAnnotation(
- ) {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence(
- ) {
- this._sequenceList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSetProperties(
- ) {
- this._sequenceSetPropertiesList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.schemabinding.version2.Annotation vAnnotation) {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Annotation removeAnnotationAt(
- final int index) {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.schemabinding.version2.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(
- final jalview.schemabinding.version2.Sequence vSequence) {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Sequence removeSequenceAt(
- final int index) {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.schemabinding.version2.Sequence) obj;
- }
-
- /**
- * Method removeSequenceSetProperties.
- *
- * @param vSequenceSetProperties
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {
- boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);
- return removed;
- }
-
- /**
- * Method removeSequenceSetPropertiesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
- final int index) {
- java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
- return (jalview.schemabinding.version2.SequenceSetProperties) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlcodonFrame(
- final int index,
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodonFrameList.size()) {
- throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
- }
-
- this._alcodonFrameList.set(index, vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param vAlcodonFrameArray
- */
- public void setAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
- //-- copy array
- _alcodonFrameList.clear();
-
- for (int i = 0; i < vAlcodonFrameArray.length; i++) {
- this._alcodonFrameList.add(vAlcodonFrameArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAnnotation(
- final int index,
- final jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size()) {
- throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
- }
-
- this._annotationList.set(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vAnnotationArray
- */
- public void setAnnotation(
- final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {
- //-- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++) {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'datasetId'. The field 'datasetId'
- * has the following description: reference to set where
- * jalview will gather the dataset sequences for all sequences
- * in the set.
- *
- *
- * @param datasetId the value of field 'datasetId'.
- */
- public void setDatasetId(
- final java.lang.String datasetId) {
- this._datasetId = datasetId;
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(
- final java.lang.String gapChar) {
- this._gapChar = gapChar;
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequence(
- final int index,
- final jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size()) {
- throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
- }
-
- this._sequenceList.set(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceArray
- */
- public void setSequence(
- final jalview.schemabinding.version2.Sequence[] vSequenceArray) {
- //-- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++) {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequenceSetProperties(
- final int index,
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
- throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
- }
-
- this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
- }
-
- /**
- *
- *
- * @param vSequenceSetPropertiesArray
- */
- public void setSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {
- //-- copy array
- _sequenceSetPropertiesList.clear();
-
- for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {
- this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceSet
- */
- public static jalview.schemabinding.version2.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class SequenceSet implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * reference to set where jalview will gather the dataset sequences for all
+ * sequences in the set.
+ *
+ */
+ private java.lang.String _datasetId;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+ /**
+ * Field _sequenceSetPropertiesList.
+ */
+ private java.util.Vector _sequenceSetPropertiesList;
+
+ /**
+ * Field _alcodonFrameList.
+ */
+ private java.util.Vector _alcodonFrameList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSet()
+ {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ this._sequenceSetPropertiesList = new java.util.Vector();
+ this._alcodonFrameList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonFrameList.addElement(vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonFrameList.add(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(final int index,
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final jalview.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(final int index,
+ final jalview.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
+ }
+
+ /**
+ * Method enumerateAlcodonFrame.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame
+ * elements
+ */
+ public java.util.Enumeration enumerateAlcodonFrame()
+ {
+ return this._alcodonFrameList.elements();
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Annotation
+ * elements
+ */
+ public java.util.Enumeration enumerateAnnotation()
+ {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Sequence
+ * elements
+ */
+ public java.util.Enumeration enumerateSequence()
+ {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSetProperties.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SequenceSetProperties elements
+ */
+ public java.util.Enumeration enumerateSequenceSetProperties()
+ {
+ return this._sequenceSetPropertiesList.elements();
+ }
+
+ /**
+ * Method getAlcodonFrame.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the
+ * given inde
+ */
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size())
+ {
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
+ .get(index);
+ }
+
+ /**
+ * Method getAlcodonFrame.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()
+ {
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlcodonFrameCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonFrameCount()
+ {
+ return this._alcodonFrameList.size();
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Annotation at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Annotation getAnnotation(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size())
+ {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+ + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Annotation) _annotationList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotation.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Annotation[] getAnnotation()
+ {
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
+ return (jalview.schemabinding.version2.Annotation[]) this._annotationList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationCount()
+ {
+ return this._annotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'datasetId'. The field 'datasetId' has the
+ * following description: reference to set where jalview will gather the
+ * dataset sequences for all sequences in the set.
+ *
+ *
+ * @return the value of field 'DatasetId'.
+ */
+ public java.lang.String getDatasetId()
+ {
+ return this._datasetId;
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar()
+ {
+ return this._gapChar;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Sequence at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Sequence getSequence(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Sequence) _sequenceList
+ .get(index);
+ }
+
+ /**
+ * Method getSequence.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Sequence[] getSequence()
+ {
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount()
+ {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method getSequenceSetProperties.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.SequenceSetProperties at the given
+ * index
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getSequenceSetProperties: Index value '" + index
+ + "' not in range [0.."
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
+ .get(index);
+ }
+
+ /**
+ * Method getSequenceSetProperties.Returns the contents of the collection in
+ * an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
+ {
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetPropertiesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetPropertiesCount()
+ {
+ return this._sequenceSetPropertiesList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlcodonFrame.
+ *
+ * @param vAlcodonFrame
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ {
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonFrameAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+ final int index)
+ {
+ java.lang.Object obj = this._alcodonFrameList.remove(index);
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlcodonFrame()
+ {
+ this._alcodonFrameList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAnnotation()
+ {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence()
+ {
+ this._sequenceList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSetProperties()
+ {
+ this._sequenceSetPropertiesList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.schemabinding.version2.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.schemabinding.version2.Sequence vSequence)
+ {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.schemabinding.version2.Sequence) obj;
+ }
+
+ /**
+ * Method removeSequenceSetProperties.
+ *
+ * @param vSequenceSetProperties
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ {
+ boolean removed = _sequenceSetPropertiesList
+ .remove(vSequenceSetProperties);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetPropertiesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
+ return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlcodonFrame(final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size())
+ {
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ this._alcodonFrameList.set(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonFrameArray
+ */
+ public void setAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)
+ {
+ // -- copy array
+ _alcodonFrameList.clear();
+
+ for (int i = 0; i < vAlcodonFrameArray.length; i++)
+ {
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotation(final int index,
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size())
+ {
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+ + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
+ }
+
+ this._annotationList.set(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationArray
+ */
+ public void setAnnotation(
+ final jalview.schemabinding.version2.Annotation[] vAnnotationArray)
+ {
+ // -- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++)
+ {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'datasetId'. The field 'datasetId' has the
+ * following description: reference to set where jalview will gather the
+ * dataset sequences for all sequences in the set.
+ *
+ *
+ * @param datasetId
+ * the value of field 'datasetId'.
+ */
+ public void setDatasetId(final java.lang.String datasetId)
+ {
+ this._datasetId = datasetId;
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar
+ * the value of field 'gapChar'.
+ */
+ public void setGapChar(final java.lang.String gapChar)
+ {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequence(final int index,
+ final jalview.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(
+ final jalview.schemabinding.version2.Sequence[] vSequenceArray)
+ {
+ // -- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++)
+ {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setSequenceSetProperties: Index value '" + index
+ + "' not in range [0.."
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetPropertiesArray
+ */
+ public void setSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)
+ {
+ // -- copy array
+ _sequenceSetPropertiesList.clear();
+
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)
+ {
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequenceSet
+ */
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceSet) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SequenceSet.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSetProperties implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _key.
- */
- private java.lang.String _key;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSetProperties() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'key'.
- *
- * @return the value of field 'Key'.
- */
- public java.lang.String getKey(
- ) {
- return this._key;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'key'.
- *
- * @param key the value of field 'key'.
- */
- public void setKey(
- final java.lang.String key) {
- this._key = key;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final java.lang.String value) {
- this._value = value;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceSetProperties
- */
- public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class SequenceSetProperties implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _key.
+ */
+ private java.lang.String _key;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSetProperties()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'key'.
+ *
+ * @return the value of field 'Key'.
+ */
+ public java.lang.String getKey()
+ {
+ return this._key;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'key'.
+ *
+ * @param key
+ * the value of field 'key'.
+ */
+ public void setKey(final java.lang.String key)
+ {
+ this._key = key;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final java.lang.String value)
+ {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.SequenceSetProperties
+ */
+ public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.SequenceSetProperties.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceType implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _sequence.
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public java.lang.String getSequence(
- ) {
- return this._sequence;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(
- final java.lang.String sequence) {
- this._sequence = sequence;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceType
- */
- public static jalview.schemabinding.version2.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceType()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence()
+ {
+ return this._sequence;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence
+ * the value of field 'sequence'.
+ */
+ public void setSequence(final java.lang.String sequence)
+ {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+ */
+ public static jalview.schemabinding.version2.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SequenceType.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Setting implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _display.
- */
- private boolean _display;
-
- /**
- * keeps track of state for field: _display
- */
- private boolean _has_display;
-
- /**
- * Field _order.
- */
- private float _order;
-
- /**
- * keeps track of state for field: _order
- */
- private boolean _has_order;
-
- /**
- * Optional minimum colour
- * for graduated
- * feature
- * colour
- *
- */
- private int _mincolour;
-
- /**
- * keeps track of state for field: _mincolour
- */
- private boolean _has_mincolour;
-
- /**
- * threshold value for
- * graduated feature colour
- *
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * threshold type for
- * graduated feature colour
- *
- */
- private int _threshstate;
-
- /**
- * keeps track of state for field: _threshstate
- */
- private boolean _has_threshstate;
-
- /**
- * Field _max.
- */
- private float _max;
-
- /**
- * keeps track of state for field: _max
- */
- private boolean _has_max;
-
- /**
- * Field _min.
- */
- private float _min;
-
- /**
- * keeps track of state for field: _min
- */
- private boolean _has_min;
-
- /**
- * Field _colourByLabel.
- */
- private boolean _colourByLabel;
-
- /**
- * keeps track of state for field: _colourByLabel
- */
- private boolean _has_colourByLabel;
-
- /**
- * Field _autoScale.
- */
- private boolean _autoScale;
-
- /**
- * keeps track of state for field: _autoScale
- */
- private boolean _has_autoScale;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Setting() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAutoScale(
- ) {
- this._has_autoScale= false;
- }
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deleteColourByLabel(
- ) {
- this._has_colourByLabel= false;
- }
-
- /**
- */
- public void deleteDisplay(
- ) {
- this._has_display= false;
- }
-
- /**
- */
- public void deleteMax(
- ) {
- this._has_max= false;
- }
-
- /**
- */
- public void deleteMin(
- ) {
- this._has_min= false;
- }
-
- /**
- */
- public void deleteMincolour(
- ) {
- this._has_mincolour= false;
- }
-
- /**
- */
- public void deleteOrder(
- ) {
- this._has_order= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- */
- public void deleteThreshstate(
- ) {
- this._has_threshstate= false;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean getAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean getColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean getDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Returns the value of field 'max'.
- *
- * @return the value of field 'Max'.
- */
- public float getMax(
- ) {
- return this._max;
- }
-
- /**
- * Returns the value of field 'min'.
- *
- * @return the value of field 'Min'.
- */
- public float getMin(
- ) {
- return this._min;
- }
-
- /**
- * Returns the value of field 'mincolour'. The field
- * 'mincolour' has the following description: Optional minimum
- * colour
- * for graduated
- * feature
- * colour
- *
- *
- * @return the value of field 'Mincolour'.
- */
- public int getMincolour(
- ) {
- return this._mincolour;
- }
-
- /**
- * Returns the value of field 'order'.
- *
- * @return the value of field 'Order'.
- */
- public float getOrder(
- ) {
- return this._order;
- }
-
- /**
- * Returns the value of field 'threshold'. The field
- * 'threshold' has the following description: threshold value
- * for
- * graduated feature colour
- *
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Returns the value of field 'threshstate'. The field
- * 'threshstate' has the following description: threshold type
- * for
- * graduated feature colour
- *
- *
- * @return the value of field 'Threshstate'.
- */
- public int getThreshstate(
- ) {
- return this._threshstate;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Method hasAutoScale.
- *
- * @return true if at least one AutoScale has been added
- */
- public boolean hasAutoScale(
- ) {
- return this._has_autoScale;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasColourByLabel.
- *
- * @return true if at least one ColourByLabel has been added
- */
- public boolean hasColourByLabel(
- ) {
- return this._has_colourByLabel;
- }
-
- /**
- * Method hasDisplay.
- *
- * @return true if at least one Display has been added
- */
- public boolean hasDisplay(
- ) {
- return this._has_display;
- }
-
- /**
- * Method hasMax.
- *
- * @return true if at least one Max has been added
- */
- public boolean hasMax(
- ) {
- return this._has_max;
- }
-
- /**
- * Method hasMin.
- *
- * @return true if at least one Min has been added
- */
- public boolean hasMin(
- ) {
- return this._has_min;
- }
-
- /**
- * Method hasMincolour.
- *
- * @return true if at least one Mincolour has been added
- */
- public boolean hasMincolour(
- ) {
- return this._has_mincolour;
- }
-
- /**
- * Method hasOrder.
- *
- * @return true if at least one Order has been added
- */
- public boolean hasOrder(
- ) {
- return this._has_order;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Method hasThreshstate.
- *
- * @return true if at least one Threshstate has been added
- */
- public boolean hasThreshstate(
- ) {
- return this._has_threshstate;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean isAutoScale(
- ) {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean isColourByLabel(
- ) {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean isDisplay(
- ) {
- return this._display;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'autoScale'.
- *
- * @param autoScale the value of field 'autoScale'.
- */
- public void setAutoScale(
- final boolean autoScale) {
- this._autoScale = autoScale;
- this._has_autoScale = true;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'colourByLabel'.
- *
- * @param colourByLabel the value of field 'colourByLabel'.
- */
- public void setColourByLabel(
- final boolean colourByLabel) {
- this._colourByLabel = colourByLabel;
- this._has_colourByLabel = true;
- }
-
- /**
- * Sets the value of field 'display'.
- *
- * @param display the value of field 'display'.
- */
- public void setDisplay(
- final boolean display) {
- this._display = display;
- this._has_display = true;
- }
-
- /**
- * Sets the value of field 'max'.
- *
- * @param max the value of field 'max'.
- */
- public void setMax(
- final float max) {
- this._max = max;
- this._has_max = true;
- }
-
- /**
- * Sets the value of field 'min'.
- *
- * @param min the value of field 'min'.
- */
- public void setMin(
- final float min) {
- this._min = min;
- this._has_min = true;
- }
-
- /**
- * Sets the value of field 'mincolour'. The field 'mincolour'
- * has the following description: Optional minimum colour
- * for graduated
- * feature
- * colour
- *
- *
- * @param mincolour the value of field 'mincolour'.
- */
- public void setMincolour(
- final int mincolour) {
- this._mincolour = mincolour;
- this._has_mincolour = true;
- }
-
- /**
- * Sets the value of field 'order'.
- *
- * @param order the value of field 'order'.
- */
- public void setOrder(
- final float order) {
- this._order = order;
- this._has_order = true;
- }
-
- /**
- * Sets the value of field 'threshold'. The field 'threshold'
- * has the following description: threshold value for
- * graduated feature colour
- *
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Sets the value of field 'threshstate'. The field
- * 'threshstate' has the following description: threshold type
- * for
- * graduated feature colour
- *
- *
- * @param threshstate the value of field 'threshstate'.
- */
- public void setThreshstate(
- final int threshstate) {
- this._threshstate = threshstate;
- this._has_threshstate = true;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Settin
- */
- public static jalview.schemabinding.version2.Setting unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Setting implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+ /**
+ * Field _order.
+ */
+ private float _order;
+
+ /**
+ * keeps track of state for field: _order
+ */
+ private boolean _has_order;
+
+ /**
+ * Optional minimum colour for graduated feature colour
+ *
+ */
+ private int _mincolour;
+
+ /**
+ * keeps track of state for field: _mincolour
+ */
+ private boolean _has_mincolour;
+
+ /**
+ * threshold value for graduated feature colour
+ *
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * threshold type for graduated feature colour
+ *
+ */
+ private int _threshstate;
+
+ /**
+ * keeps track of state for field: _threshstate
+ */
+ private boolean _has_threshstate;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Setting()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAutoScale()
+ {
+ this._has_autoScale = false;
+ }
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel()
+ {
+ this._has_colourByLabel = false;
+ }
+
+ /**
+ */
+ public void deleteDisplay()
+ {
+ this._has_display = false;
+ }
+
+ /**
+ */
+ public void deleteMax()
+ {
+ this._has_max = false;
+ }
+
+ /**
+ */
+ public void deleteMin()
+ {
+ this._has_min = false;
+ }
+
+ /**
+ */
+ public void deleteMincolour()
+ {
+ this._has_mincolour = false;
+ }
+
+ /**
+ */
+ public void deleteOrder()
+ {
+ this._has_order = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ */
+ public void deleteThreshstate()
+ {
+ this._has_threshstate = false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax()
+ {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin()
+ {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'mincolour'. The field 'mincolour' has the
+ * following description: Optional minimum colour for graduated feature colour
+ *
+ *
+ * @return the value of field 'Mincolour'.
+ */
+ public int getMincolour()
+ {
+ return this._mincolour;
+ }
+
+ /**
+ * Returns the value of field 'order'.
+ *
+ * @return the value of field 'Order'.
+ */
+ public float getOrder()
+ {
+ return this._order;
+ }
+
+ /**
+ * Returns the value of field 'threshold'. The field 'threshold' has the
+ * following description: threshold value for graduated feature colour
+ *
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'threshstate'. The field 'threshstate' has the
+ * following description: threshold type for graduated feature colour
+ *
+ *
+ * @return the value of field 'Threshstate'.
+ */
+ public int getThreshstate()
+ {
+ return this._threshstate;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale()
+ {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel()
+ {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay()
+ {
+ return this._has_display;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax()
+ {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin()
+ {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasMincolour.
+ *
+ * @return true if at least one Mincolour has been added
+ */
+ public boolean hasMincolour()
+ {
+ return this._has_mincolour;
+ }
+
+ /**
+ * Method hasOrder.
+ *
+ * @return true if at least one Order has been added
+ */
+ public boolean hasOrder()
+ {
+ return this._has_order;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasThreshstate.
+ *
+ * @return true if at least one Threshstate has been added
+ */
+ public boolean hasThreshstate()
+ {
+ return this._has_threshstate;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale
+ * the value of field 'autoScale'.
+ */
+ public void setAutoScale(final boolean autoScale)
+ {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel
+ * the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(final boolean colourByLabel)
+ {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display
+ * the value of field 'display'.
+ */
+ public void setDisplay(final boolean display)
+ {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max
+ * the value of field 'max'.
+ */
+ public void setMax(final float max)
+ {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min
+ * the value of field 'min'.
+ */
+ public void setMin(final float min)
+ {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'mincolour'. The field 'mincolour' has the
+ * following description: Optional minimum colour for graduated feature colour
+ *
+ *
+ * @param mincolour
+ * the value of field 'mincolour'.
+ */
+ public void setMincolour(final int mincolour)
+ {
+ this._mincolour = mincolour;
+ this._has_mincolour = true;
+ }
+
+ /**
+ * Sets the value of field 'order'.
+ *
+ * @param order
+ * the value of field 'order'.
+ */
+ public void setOrder(final float order)
+ {
+ this._order = order;
+ this._has_order = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'. The field 'threshold' has the
+ * following description: threshold value for graduated feature colour
+ *
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'threshstate'. The field 'threshstate' has the
+ * following description: threshold type for graduated feature colour
+ *
+ *
+ * @param threshstate
+ * the value of field 'threshstate'.
+ */
+ public void setThreshstate(final int threshstate)
+ {
+ this._threshstate = threshstate;
+ this._has_threshstate = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Settin
+ */
+ public static jalview.schemabinding.version2.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Setting.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class StructureState implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
- /**
- * Field _visible.
- */
- private boolean _visible;
-
- /**
- * keeps track of state for field: _visible
- */
- private boolean _has_visible;
-
- /**
- * additional
- * identifier
- * which
- * properly
- * disambiguates
- * the
- * structure
- * view
- * from
- * any
- * other
- * view
- * with
- * the
- * same
- * attributes.
- * This
- * is
- * not
- * an
- * ID,
- * because
- * it
- * is
- * possible
- * to
- * have
- * many
- * references
- * to
- * the
- * same
- * physical
- * structure
- * view
- * from
- * different
- * sequences
- * in
- * an
- * alignment.
- * A
- * structureState
- * element
- * citing
- * the
- * same
- * viewId
- * will
- * appear
- * for
- * each
- * instance.
- *
- */
- private java.lang.String _viewId;
-
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- */
- private boolean _alignwithAlignPanel = true;
-
- /**
- * keeps track of state for field: _alignwithAlignPanel
- */
- private boolean _has_alignwithAlignPanel;
-
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- */
- private boolean _colourwithAlignPanel = false;
-
- /**
- * keeps track of state for field: _colourwithAlignPanel
- */
- private boolean _has_colourwithAlignPanel;
-
- /**
- * Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- */
- private boolean _colourByJmol = true;
-
- /**
- * keeps track of state for field: _colourByJmol
- */
- private boolean _has_colourByJmol;
-
- /**
- * An
- * identifier
- * for
- * the
- * viewer
- * type,
- * currently
- * either
- * JMOL
- * or
- * CHIMERA
- *
- */
- private java.lang.String _type;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public StructureState() {
- super();
- setContent("");
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAlignwithAlignPanel(
- ) {
- this._has_alignwithAlignPanel= false;
- }
-
- /**
- */
- public void deleteColourByJmol(
- ) {
- this._has_colourByJmol= false;
- }
-
- /**
- */
- public void deleteColourwithAlignPanel(
- ) {
- this._has_colourwithAlignPanel= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteVisible(
- ) {
- this._has_visible= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Returns the value of field 'alignwithAlignPanel'. The field
- * 'alignwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- *
- * @return the value of field 'AlignwithAlignPanel'.
- */
- public boolean getAlignwithAlignPanel(
- ) {
- return this._alignwithAlignPanel;
- }
-
- /**
- * Returns the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- *
- * @return the value of field 'ColourByJmol'.
- */
- public boolean getColourByJmol(
- ) {
- return this._colourByJmol;
- }
-
- /**
- * Returns the value of field 'colourwithAlignPanel'. The field
- * 'colourwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- *
- * @return the value of field 'ColourwithAlignPanel'.
- */
- public boolean getColourwithAlignPanel(
- ) {
- return this._colourwithAlignPanel;
- }
-
- /**
- * Returns the value of field 'content'. The field 'content'
- * has the following description: internal content storage
- *
- * @return the value of field 'Content'.
- */
- public java.lang.String getContent(
- ) {
- return this._content;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Returns the value of field 'type'. The field 'type' has the
- * following description: An
- * identifier
- * for
- * the
- * viewer
- * type,
- * currently
- * either
- * JMOL
- * or
- * CHIMERA
- *
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType(
- ) {
- return this._type;
- }
-
- /**
- * Returns the value of field 'viewId'. The field 'viewId' has
- * the following description: additional
- * identifier
- * which
- * properly
- * disambiguates
- * the
- * structure
- * view
- * from
- * any
- * other
- * view
- * with
- * the
- * same
- * attributes.
- * This
- * is
- * not
- * an
- * ID,
- * because
- * it
- * is
- * possible
- * to
- * have
- * many
- * references
- * to
- * the
- * same
- * physical
- * structure
- * view
- * from
- * different
- * sequences
- * in
- * an
- * alignment.
- * A
- * structureState
- * element
- * citing
- * the
- * same
- * viewId
- * will
- * appear
- * for
- * each
- * instance.
- *
- *
- * @return the value of field 'ViewId'.
- */
- public java.lang.String getViewId(
- ) {
- return this._viewId;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean getVisible(
- ) {
- return this._visible;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasAlignwithAlignPanel.
- *
- * @return true if at least one AlignwithAlignPanel has been
- * added
- */
- public boolean hasAlignwithAlignPanel(
- ) {
- return this._has_alignwithAlignPanel;
- }
-
- /**
- * Method hasColourByJmol.
- *
- * @return true if at least one ColourByJmol has been added
- */
- public boolean hasColourByJmol(
- ) {
- return this._has_colourByJmol;
- }
-
- /**
- * Method hasColourwithAlignPanel.
- *
- * @return true if at least one ColourwithAlignPanel has been
- * added
- */
- public boolean hasColourwithAlignPanel(
- ) {
- return this._has_colourwithAlignPanel;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasVisible.
- *
- * @return true if at least one Visible has been added
- */
- public boolean hasVisible(
- ) {
- return this._has_visible;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'alignwithAlignPanel'. The field
- * 'alignwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- *
- * @return the value of field 'AlignwithAlignPanel'.
- */
- public boolean isAlignwithAlignPanel(
- ) {
- return this._alignwithAlignPanel;
- }
-
- /**
- * Returns the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- *
- * @return the value of field 'ColourByJmol'.
- */
- public boolean isColourByJmol(
- ) {
- return this._colourByJmol;
- }
-
- /**
- * Returns the value of field 'colourwithAlignPanel'. The field
- * 'colourwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- *
- * @return the value of field 'ColourwithAlignPanel'.
- */
- public boolean isColourwithAlignPanel(
- ) {
- return this._colourwithAlignPanel;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean isVisible(
- ) {
- return this._visible;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'alignwithAlignPanel'. The field
- * 'alignwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- *
- * @param alignwithAlignPanel the value of field
- * 'alignwithAlignPanel'.
- */
- public void setAlignwithAlignPanel(
- final boolean alignwithAlignPanel) {
- this._alignwithAlignPanel = alignwithAlignPanel;
- this._has_alignwithAlignPanel = true;
- }
-
- /**
- * Sets the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- *
- * @param colourByJmol the value of field 'colourByJmol'.
- */
- public void setColourByJmol(
- final boolean colourByJmol) {
- this._colourByJmol = colourByJmol;
- this._has_colourByJmol = true;
- }
-
- /**
- * Sets the value of field 'colourwithAlignPanel'. The field
- * 'colourwithAlignPanel' has the following description: Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- *
- * @param colourwithAlignPanel the value of field
- * 'colourwithAlignPanel'.
- */
- public void setColourwithAlignPanel(
- final boolean colourwithAlignPanel) {
- this._colourwithAlignPanel = colourwithAlignPanel;
- this._has_colourwithAlignPanel = true;
- }
-
- /**
- * Sets the value of field 'content'. The field 'content' has
- * the following description: internal content storage
- *
- * @param content the value of field 'content'.
- */
- public void setContent(
- final java.lang.String content) {
- this._content = content;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'type'. The field 'type' has the
- * following description: An
- * identifier
- * for
- * the
- * viewer
- * type,
- * currently
- * either
- * JMOL
- * or
- * CHIMERA
- *
- *
- * @param type the value of field 'type'.
- */
- public void setType(
- final java.lang.String type) {
- this._type = type;
- }
-
- /**
- * Sets the value of field 'viewId'. The field 'viewId' has the
- * following description: additional
- * identifier
- * which
- * properly
- * disambiguates
- * the
- * structure
- * view
- * from
- * any
- * other
- * view
- * with
- * the
- * same
- * attributes.
- * This
- * is
- * not
- * an
- * ID,
- * because
- * it
- * is
- * possible
- * to
- * have
- * many
- * references
- * to
- * the
- * same
- * physical
- * structure
- * view
- * from
- * different
- * sequences
- * in
- * an
- * alignment.
- * A
- * structureState
- * element
- * citing
- * the
- * same
- * viewId
- * will
- * appear
- * for
- * each
- * instance.
- *
- *
- * @param viewId the value of field 'viewId'.
- */
- public void setViewId(
- final java.lang.String viewId) {
- this._viewId = viewId;
- }
-
- /**
- * Sets the value of field 'visible'.
- *
- * @param visible the value of field 'visible'.
- */
- public void setVisible(
- final boolean visible) {
- this._visible = visible;
- this._has_visible = true;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.StructureState
- */
- public static jalview.schemabinding.version2.StructureState unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class StructureState implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * additional identifier which properly disambiguates the structure view from
+ * any other view with the same attributes. This is not an ID, because it is
+ * possible to have many references to the same physical structure view from
+ * different sequences in an alignment. A structureState element citing the
+ * same viewId will appear for each instance.
+ *
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be included in
+ * those used to perform a structure superposition (since Jalview 2.7).
+ *
+ */
+ private boolean _alignwithAlignPanel = true;
+
+ /**
+ * keeps track of state for field: _alignwithAlignPanel
+ */
+ private boolean _has_alignwithAlignPanel;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be included in
+ * those used to colour its associated sequences in this structureState(since
+ * Jalview 2.7).
+ *
+ */
+ private boolean _colourwithAlignPanel = false;
+
+ /**
+ * keeps track of state for field: _colourwithAlignPanel
+ */
+ private boolean _has_colourwithAlignPanel;
+
+ /**
+ * Flag set if the structure display is coloured by the Jmol state, rather
+ * than by one or more linked alignment views.
+ *
+ */
+ private boolean _colourByJmol = true;
+
+ /**
+ * keeps track of state for field: _colourByJmol
+ */
+ private boolean _has_colourByJmol;
+
+ /**
+ * An identifier for the viewer type, currently either JMOL or CHIMERA
+ *
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public StructureState()
+ {
+ super();
+ setContent("");
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAlignwithAlignPanel()
+ {
+ this._has_alignwithAlignPanel = false;
+ }
+
+ /**
+ */
+ public void deleteColourByJmol()
+ {
+ this._has_colourByJmol = false;
+ }
+
+ /**
+ */
+ public void deleteColourwithAlignPanel()
+ {
+ this._has_colourwithAlignPanel = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteVisible()
+ {
+ this._has_visible = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean getAlignwithAlignPanel()
+ {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean getColourByJmol()
+ {
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean getColourwithAlignPanel()
+ {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @return the value of field 'Content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'type'. The field 'type' has the following
+ * description: An identifier for the viewer type, currently either JMOL or
+ * CHIMERA
+ *
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Returns the value of field 'viewId'. The field 'viewId' has the following
+ * description: additional identifier which properly disambiguates the
+ * structure view from any other view with the same attributes. This is not an
+ * ID, because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A structureState
+ * element citing the same viewId will appear for each instance.
+ *
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId()
+ {
+ return this._viewId;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasAlignwithAlignPanel.
+ *
+ * @return true if at least one AlignwithAlignPanel has been added
+ */
+ public boolean hasAlignwithAlignPanel()
+ {
+ return this._has_alignwithAlignPanel;
+ }
+
+ /**
+ * Method hasColourByJmol.
+ *
+ * @return true if at least one ColourByJmol has been added
+ */
+ public boolean hasColourByJmol()
+ {
+ return this._has_colourByJmol;
+ }
+
+ /**
+ * Method hasColourwithAlignPanel.
+ *
+ * @return true if at least one ColourwithAlignPanel has been added
+ */
+ public boolean hasColourwithAlignPanel()
+ {
+ return this._has_colourwithAlignPanel;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean isAlignwithAlignPanel()
+ {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean isColourByJmol()
+ {
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean isColourwithAlignPanel()
+ {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @param alignwithAlignPanel
+ * the value of field 'alignwithAlignPanel'.
+ */
+ public void setAlignwithAlignPanel(final boolean alignwithAlignPanel)
+ {
+ this._alignwithAlignPanel = alignwithAlignPanel;
+ this._has_alignwithAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @param colourByJmol
+ * the value of field 'colourByJmol'.
+ */
+ public void setColourByJmol(final boolean colourByJmol)
+ {
+ this._colourByJmol = colourByJmol;
+ this._has_colourByJmol = true;
+ }
+
+ /**
+ * Sets the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @param colourwithAlignPanel
+ * the value of field 'colourwithAlignPanel'.
+ */
+ public void setColourwithAlignPanel(final boolean colourwithAlignPanel)
+ {
+ this._colourwithAlignPanel = colourwithAlignPanel;
+ this._has_colourwithAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @param content
+ * the value of field 'content'.
+ */
+ public void setContent(final java.lang.String content)
+ {
+ this._content = content;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'type'. The field 'type' has the following
+ * description: An identifier for the viewer type, currently either JMOL or
+ * CHIMERA
+ *
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * Sets the value of field 'viewId'. The field 'viewId' has the following
+ * description: additional identifier which properly disambiguates the
+ * structure view from any other view with the same attributes. This is not an
+ * ID, because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A structureState
+ * element citing the same viewId will appear for each instance.
+ *
+ *
+ * @param viewId
+ * the value of field 'viewId'.
+ */
+ public void setViewId(final java.lang.String viewId)
+ {
+ this._viewId = viewId;
+ }
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible
+ * the value of field 'visible'.
+ */
+ public void setVisible(final boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.StructureState
+ */
+ public static jalview.schemabinding.version2.StructureState unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.StructureState) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.StructureState.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class ThresholdLine implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _value.
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ThresholdLine() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteColour(
- ) {
- this._has_colour= false;
- }
-
- /**
- */
- public void deleteValue(
- ) {
- this._has_value= false;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'label'.
- *
- * @return the value of field 'Label'.
- */
- public java.lang.String getLabel(
- ) {
- return this._label;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public float getValue(
- ) {
- return this._value;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour(
- ) {
- return this._has_colour;
- }
-
- /**
- * Method hasValue.
- *
- * @return true if at least one Value has been added
- */
- public boolean hasValue(
- ) {
- return this._has_value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final int colour) {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'label'.
- *
- * @param label the value of field 'label'.
- */
- public void setLabel(
- final java.lang.String label) {
- this._label = label;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(
- final float value) {
- this._value = value;
- this._has_value = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.ThresholdLine
- */
- public static jalview.schemabinding.version2.ThresholdLine unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class ThresholdLine implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public ThresholdLine()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteValue()
+ {
+ this._has_value = false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue()
+ {
+ return this._value;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue()
+ {
+ return this._has_value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label
+ * the value of field 'label'.
+ */
+ public void setLabel(final java.lang.String label)
+ {
+ this._label = label;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value
+ * the value of field 'value'.
+ */
+ public void setValue(final float value)
+ {
+ this._value = value;
+ this._has_value = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.ThresholdLine
+ */
+ public static jalview.schemabinding.version2.ThresholdLine unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.ThresholdLine.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Tree implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _showBootstrap.
- */
- private boolean _showBootstrap;
-
- /**
- * keeps track of state for field: _showBootstrap
- */
- private boolean _has_showBootstrap;
-
- /**
- * Field _showDistances.
- */
- private boolean _showDistances;
-
- /**
- * keeps track of state for field: _showDistances
- */
- private boolean _has_showDistances;
-
- /**
- * Field _markUnlinked.
- */
- private boolean _markUnlinked;
-
- /**
- * keeps track of state for field: _markUnlinked
- */
- private boolean _has_markUnlinked;
-
- /**
- * Field _fitToWindow.
- */
- private boolean _fitToWindow;
-
- /**
- * keeps track of state for field: _fitToWindow
- */
- private boolean _has_fitToWindow;
-
- /**
- * Field _currentTree.
- */
- private boolean _currentTree;
-
- /**
- * keeps track of state for field: _currentTree
- */
- private boolean _has_currentTree;
-
- /**
- * Tree ID added for binding tree
- * visualization
- * settings to vamsas
- * document trees in jalview 2.4.1
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newick.
- */
- private java.lang.String _newick;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteCurrentTree(
- ) {
- this._has_currentTree= false;
- }
-
- /**
- */
- public void deleteFitToWindow(
- ) {
- this._has_fitToWindow= false;
- }
-
- /**
- */
- public void deleteFontSize(
- ) {
- this._has_fontSize= false;
- }
-
- /**
- */
- public void deleteFontStyle(
- ) {
- this._has_fontStyle= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteMarkUnlinked(
- ) {
- this._has_markUnlinked= false;
- }
-
- /**
- */
- public void deleteShowBootstrap(
- ) {
- this._has_showBootstrap= false;
- }
-
- /**
- */
- public void deleteShowDistances(
- ) {
- this._has_showDistances= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean getCurrentTree(
- ) {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean getFitToWindow(
- ) {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName(
- ) {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize(
- ) {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle(
- ) {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Tree ID added for binding tree
- * visualization
- * settings to vamsas
- * document trees in jalview 2.4.1
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean getMarkUnlinked(
- ) {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return the value of field 'Newick'.
- */
- public java.lang.String getNewick(
- ) {
- return this._newick;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean getShowBootstrap(
- ) {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean getShowDistances(
- ) {
- return this._showDistances;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasCurrentTree.
- *
- * @return true if at least one CurrentTree has been added
- */
- public boolean hasCurrentTree(
- ) {
- return this._has_currentTree;
- }
-
- /**
- * Method hasFitToWindow.
- *
- * @return true if at least one FitToWindow has been added
- */
- public boolean hasFitToWindow(
- ) {
- return this._has_fitToWindow;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize(
- ) {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle(
- ) {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasMarkUnlinked.
- *
- * @return true if at least one MarkUnlinked has been added
- */
- public boolean hasMarkUnlinked(
- ) {
- return this._has_markUnlinked;
- }
-
- /**
- * Method hasShowBootstrap.
- *
- * @return true if at least one ShowBootstrap has been added
- */
- public boolean hasShowBootstrap(
- ) {
- return this._has_showBootstrap;
- }
-
- /**
- * Method hasShowDistances.
- *
- * @return true if at least one ShowDistances has been added
- */
- public boolean hasShowDistances(
- ) {
- return this._has_showDistances;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean isCurrentTree(
- ) {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean isFitToWindow(
- ) {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean isMarkUnlinked(
- ) {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean isShowBootstrap(
- ) {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean isShowDistances(
- ) {
- return this._showDistances;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'currentTree'.
- *
- * @param currentTree the value of field 'currentTree'.
- */
- public void setCurrentTree(
- final boolean currentTree) {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- }
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow the value of field 'fitToWindow'.
- */
- public void setFitToWindow(
- final boolean fitToWindow) {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(
- final java.lang.String fontName) {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(
- final int fontSize) {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(
- final int fontStyle) {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Tree ID added for binding tree
- * visualization
- * settings to vamsas
- * document trees in jalview 2.4.1
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(
- final boolean markUnlinked) {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- }
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick the value of field 'newick'.
- */
- public void setNewick(
- final java.lang.String newick) {
- this._newick = newick;
- }
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(
- final boolean showBootstrap) {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- }
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances the value of field 'showDistances'.
- */
- public void setShowDistances(
- final boolean showDistances) {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Tree
- */
- public static jalview.schemabinding.version2.Tree unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Tree implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Tree ID added for binding tree visualization settings to vamsas document
+ * trees in jalview 2.4.1
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Tree()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteCurrentTree()
+ {
+ this._has_currentTree = false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow()
+ {
+ this._has_fitToWindow = false;
+ }
+
+ /**
+ */
+ public void deleteFontSize()
+ {
+ this._has_fontSize = false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle()
+ {
+ this._has_fontStyle = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked()
+ {
+ this._has_markUnlinked = false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap()
+ {
+ this._has_showBootstrap = false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances()
+ {
+ this._has_showDistances = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree()
+ {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow()
+ {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Tree ID added for binding tree visualization settings to
+ * vamsas document trees in jalview 2.4.1
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked()
+ {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick()
+ {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap()
+ {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances()
+ {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree()
+ {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow()
+ {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked()
+ {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap()
+ {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances()
+ {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree()
+ {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow()
+ {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked()
+ {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap()
+ {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances()
+ {
+ return this._showDistances;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree
+ * the value of field 'currentTree'.
+ */
+ public void setCurrentTree(final boolean currentTree)
+ {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow
+ * the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(final boolean fitToWindow)
+ {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Tree ID added for binding tree visualization settings to vamsas document
+ * trees in jalview 2.4.1
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked
+ * the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(final boolean markUnlinked)
+ {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick
+ * the value of field 'newick'.
+ */
+ public void setNewick(final java.lang.String newick)
+ {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap
+ * the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(final boolean showBootstrap)
+ {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances
+ * the value of field 'showDistances'.
+ */
+ public void setShowDistances(final boolean showDistances)
+ {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Tree
+ */
+ public static jalview.schemabinding.version2.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Tree.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColourScheme extends JalviewUserColours
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+ java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColourScheme() {
- super();
- }
-
+ public UserColourScheme()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.JalviewUserColours
- */
- public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+ */
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.UserColourScheme.class,
+ reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _userColourScheme.
- */
- private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColours() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'userColourScheme'.
- *
- * @return the value of field 'UserColourScheme'.
- */
- public jalview.schemabinding.version2.UserColourScheme getUserColourScheme(
- ) {
- return this._userColourScheme;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'userColourScheme'.
- *
- * @param userColourScheme the value of field 'userColourScheme'
- */
- public void setUserColourScheme(
- final jalview.schemabinding.version2.UserColourScheme userColourScheme) {
- this._userColourScheme = userColourScheme;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.UserColours
- */
- public static jalview.schemabinding.version2.UserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _userColourScheme.
+ */
+ private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public UserColours()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'userColourScheme'.
+ *
+ * @return the value of field 'UserColourScheme'.
+ */
+ public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+ {
+ return this._userColourScheme;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'userColourScheme'.
+ *
+ * @param userColourScheme
+ * the value of field 'userColourScheme'
+ */
+ public void setUserColourScheme(
+ final jalview.schemabinding.version2.UserColourScheme userColourScheme)
+ {
+ this._userColourScheme = userColourScheme;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.UserColours
+ */
+ public static jalview.schemabinding.version2.UserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.UserColours) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.UserColours.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VAMSAS implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList.
- */
- private java.util.Vector _sequenceSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS() {
- super();
- this._treeList = new java.util.Vector();
- this._sequenceSetList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSet(
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetList.addElement(vSequenceSet);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSet(
- final int index,
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetList.add(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- * Method enumerateSequenceSet.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.SequenceSet elements
- */
- public java.util.Enumeration enumerateSequenceSet(
- ) {
- return this._sequenceSetList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
- }
-
- /**
- * Method getSequenceSet.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.SequenceSet at the given index
- */
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size()) {
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);
- }
-
- /**
- * Method getSequenceSet.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(
- ) {
- jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
- return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);
- }
-
- /**
- * Method getSequenceSetCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetCount(
- ) {
- return this._sequenceSetList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (java.lang.String) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getTree(
- ) {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllSequenceSet(
- ) {
- this._sequenceSetList.clear();
+public class VAMSAS implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VAMSAS()
+ {
+ super();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetList.addElement(vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSet(final int index,
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetList.add(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index, final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateSequenceSet.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet
+ * elements
+ */
+ public java.util.Enumeration enumerateSequenceSet()
+ {
+ return this._sequenceSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method getSequenceSet.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.SequenceSet at the
+ * given index
+ */
+ public jalview.schemabinding.version2.SequenceSet getSequenceSet(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceSetList.size() - 1) + "]");
}
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- * Method removeSequenceSet.
- *
- * @param vSequenceSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSet(
- final jalview.schemabinding.version2.SequenceSet vSequenceSet) {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
- final int index) {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (jalview.schemabinding.version2.SequenceSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final java.lang.String vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
+ return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList
+ .get(index);
+ }
+
+ /**
+ * Method getSequenceSet.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+ {
+ jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+ return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetCount()
+ {
+ return this._sequenceSetList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
}
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (java.lang.String) obj;
+ return (java.lang.String) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getTree()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount()
+ {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequenceSet(
- final int index,
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size()) {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
- }
-
- this._sequenceSetList.set(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vSequenceSetArray
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setSequenceSet(
- final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {
- //-- copy array
- _sequenceSetList.clear();
-
- for (int i = 0; i < vSequenceSetArray.length; i++) {
- this._sequenceSetList.add(vSequenceSetArray[i]);
- }
- }
+ public void removeAllSequenceSet()
+ {
+ this._sequenceSetList.clear();
+ }
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
+ /**
*/
- public void setTree(
- final int index,
- final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+ {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (jalview.schemabinding.version2.SequenceSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final java.lang.String vTree)
+ {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeTreeAt(final int index)
+ {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceSet(final int index,
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceSetList.size() - 1) + "]");
}
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final java.lang.String[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
- }
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)
+ {
+ // -- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++)
+ {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
}
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
- */
- public static jalview.schemabinding.version2.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index, final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
}
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final java.lang.String[] vTreeArray)
+ {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++)
+ {
+ this._treeList.add(vTreeArray[i]);
}
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+ */
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.VAMSAS.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VamsasModel extends VAMSAS
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
{
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VamsasModel() {
- super();
- }
-
+ public VamsasModel()
+ {
+ super();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
- */
- public static jalview.schemabinding.version2.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+ */
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.VamsasModel.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
-
- /**
- * Field _rightAlignIds.
- */
- private boolean _rightAlignIds;
-
- /**
- * keeps track of state for field: _rightAlignIds
- */
- private boolean _has_rightAlignIds;
-
- /**
- * Field _showText.
- */
- private boolean _showText;
-
- /**
- * keeps track of state for field: _showText
- */
- private boolean _has_showText;
-
- /**
- * Field _showColourText.
- */
- private boolean _showColourText;
-
- /**
- * keeps track of state for field: _showColourText
- */
- private boolean _has_showColourText;
-
- /**
- * Field _showUnconserved.
- */
- private boolean _showUnconserved = false;
-
- /**
- * keeps track of state for field: _showUnconserved
- */
- private boolean _has_showUnconserved;
-
- /**
- * Field _showBoxes.
- */
- private boolean _showBoxes;
-
- /**
- * keeps track of state for field: _showBoxes
- */
- private boolean _has_showBoxes;
-
- /**
- * Field _wrapAlignment.
- */
- private boolean _wrapAlignment;
-
- /**
- * keeps track of state for field: _wrapAlignment
- */
- private boolean _has_wrapAlignment;
-
- /**
- * Field _renderGaps.
- */
- private boolean _renderGaps;
-
- /**
- * keeps track of state for field: _renderGaps
- */
- private boolean _has_renderGaps;
-
- /**
- * Field _showSequenceFeatures.
- */
- private boolean _showSequenceFeatures;
-
- /**
- * keeps track of state for field: _showSequenceFeatures
- */
- private boolean _has_showSequenceFeatures;
-
- /**
- * Field _showNPfeatureTooltip.
- */
- private boolean _showNPfeatureTooltip;
-
- /**
- * keeps track of state for field: _showNPfeatureTooltip
- */
- private boolean _has_showNPfeatureTooltip;
-
- /**
- * Field _showDbRefTooltip.
- */
- private boolean _showDbRefTooltip;
-
- /**
- * keeps track of state for field: _showDbRefTooltip
- */
- private boolean _has_showDbRefTooltip;
-
- /**
- * Field _followHighlight.
- */
- private boolean _followHighlight = true;
-
- /**
- * keeps track of state for field: _followHighlight
- */
- private boolean _has_followHighlight;
-
- /**
- * Field _followSelection.
- */
- private boolean _followSelection = true;
-
- /**
- * keeps track of state for field: _followSelection
- */
- private boolean _has_followSelection;
-
- /**
- * Field _showAnnotation.
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * Field _centreColumnLabels.
- */
- private boolean _centreColumnLabels = false;
-
- /**
- * keeps track of state for field: _centreColumnLabels
- */
- private boolean _has_centreColumnLabels;
-
- /**
- * Field _showGroupConservation.
- */
- private boolean _showGroupConservation = false;
-
- /**
- * keeps track of state for field: _showGroupConservation
- */
- private boolean _has_showGroupConservation;
-
- /**
- * Field _showGroupConsensus.
- */
- private boolean _showGroupConsensus = false;
-
- /**
- * keeps track of state for field: _showGroupConsensus
- */
- private boolean _has_showGroupConsensus;
-
- /**
- * Field _showConsensusHistogram.
- */
- private boolean _showConsensusHistogram = true;
-
- /**
- * keeps track of state for field: _showConsensusHistogram
- */
- private boolean _has_showConsensusHistogram;
-
- /**
- * Field _showSequenceLogo.
- */
- private boolean _showSequenceLogo = false;
-
- /**
- * keeps track of state for field: _showSequenceLogo
- */
- private boolean _has_showSequenceLogo;
-
- /**
- * Field _normaliseSequenceLogo.
- */
- private boolean _normaliseSequenceLogo = false;
-
- /**
- * keeps track of state for field: _normaliseSequenceLogo
- */
- private boolean _has_normaliseSequenceLogo;
-
- /**
- * Field _ignoreGapsinConsensus.
- */
- private boolean _ignoreGapsinConsensus = true;
-
- /**
- * keeps track of state for field: _ignoreGapsinConsensus
- */
- private boolean _has_ignoreGapsinConsensus;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _scaleProteinAsCdna.
- */
- private boolean _scaleProteinAsCdna = true;
-
- /**
- * keeps track of state for field: _scaleProteinAsCdna
- */
- private boolean _has_scaleProteinAsCdna;
-
- /**
- * Field _viewName.
- */
- private java.lang.String _viewName;
-
- /**
- * Field _sequenceSetId.
- */
- private java.lang.String _sequenceSetId;
-
- /**
- * Field _gatheredViews.
- */
- private boolean _gatheredViews;
-
- /**
- * keeps track of state for field: _gatheredViews
- */
- private boolean _has_gatheredViews;
-
- /**
- * Field _textCol1.
- */
- private int _textCol1;
-
- /**
- * keeps track of state for field: _textCol1
- */
- private boolean _has_textCol1;
-
- /**
- * Field _textCol2.
- */
- private int _textCol2;
-
- /**
- * keeps track of state for field: _textCol2
- */
- private boolean _has_textCol2;
-
- /**
- * Field _textColThreshold.
- */
- private int _textColThreshold;
-
- /**
- * keeps track of state for field: _textColThreshold
- */
- private boolean _has_textColThreshold;
-
- /**
- * unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- */
- private java.lang.String _id;
-
- /**
- * The viewport id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- */
- private java.lang.String _complementId;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _annotationColours.
- */
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
- /**
- * Field _hiddenColumnsList.
- */
- private java.util.Vector _hiddenColumnsList;
-
- /**
- * Field _calcIdParamList.
- */
- private java.util.Vector _calcIdParamList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Viewport() {
- super();
- this._hiddenColumnsList = new java.util.Vector();
- this._calcIdParamList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- this._calcIdParamList.addElement(vCalcIdParam);
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addCalcIdParam(
- final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- this._calcIdParamList.add(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenColumnsList.addElement(vHiddenColumns);
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenColumns(
- final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenColumnsList.add(index, vHiddenColumns);
- }
+public class Viewport implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _rightAlignIds.
+ */
+ private boolean _rightAlignIds;
+
+ /**
+ * keeps track of state for field: _rightAlignIds
+ */
+ private boolean _has_rightAlignIds;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showUnconserved.
+ */
+ private boolean _showUnconserved = false;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showNPfeatureTooltip.
+ */
+ private boolean _showNPfeatureTooltip;
+
+ /**
+ * keeps track of state for field: _showNPfeatureTooltip
+ */
+ private boolean _has_showNPfeatureTooltip;
+
+ /**
+ * Field _showDbRefTooltip.
+ */
+ private boolean _showDbRefTooltip;
+
+ /**
+ * keeps track of state for field: _showDbRefTooltip
+ */
+ private boolean _has_showDbRefTooltip;
+
+ /**
+ * Field _followHighlight.
+ */
+ private boolean _followHighlight = true;
+
+ /**
+ * keeps track of state for field: _followHighlight
+ */
+ private boolean _has_followHighlight;
+
+ /**
+ * Field _followSelection.
+ */
+ private boolean _followSelection = true;
+
+ /**
+ * keeps track of state for field: _followSelection
+ */
+ private boolean _has_followSelection;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _centreColumnLabels.
+ */
+ private boolean _centreColumnLabels = false;
+
+ /**
+ * keeps track of state for field: _centreColumnLabels
+ */
+ private boolean _has_centreColumnLabels;
+
+ /**
+ * Field _showGroupConservation.
+ */
+ private boolean _showGroupConservation = false;
+
+ /**
+ * keeps track of state for field: _showGroupConservation
+ */
+ private boolean _has_showGroupConservation;
+
+ /**
+ * Field _showGroupConsensus.
+ */
+ private boolean _showGroupConsensus = false;
+
+ /**
+ * keeps track of state for field: _showGroupConsensus
+ */
+ private boolean _has_showGroupConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _scaleProteinAsCdna.
+ */
+ private boolean _scaleProteinAsCdna = true;
+
+ /**
+ * keeps track of state for field: _scaleProteinAsCdna
+ */
+ private boolean _has_scaleProteinAsCdna;
+
+ /**
+ * Field _viewName.
+ */
+ private java.lang.String _viewName;
+
+ /**
+ * Field _sequenceSetId.
+ */
+ private java.lang.String _sequenceSetId;
+
+ /**
+ * Field _gatheredViews.
+ */
+ private boolean _gatheredViews;
+
+ /**
+ * keeps track of state for field: _gatheredViews
+ */
+ private boolean _has_gatheredViews;
+
+ /**
+ * Field _textCol1.
+ */
+ private int _textCol1;
+
+ /**
+ * keeps track of state for field: _textCol1
+ */
+ private boolean _has_textCol1;
+
+ /**
+ * Field _textCol2.
+ */
+ private int _textCol2;
+
+ /**
+ * keeps track of state for field: _textCol2
+ */
+ private boolean _has_textCol2;
+
+ /**
+ * Field _textColThreshold.
+ */
+ private int _textColThreshold;
+
+ /**
+ * keeps track of state for field: _textColThreshold
+ */
+ private boolean _has_textColThreshold;
+
+ /**
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * The viewport id of this viewport's (cdna/protein) coding complement, if any
+ *
+ */
+ private java.lang.String _complementId;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ /**
+ * Field _hiddenColumnsList.
+ */
+ private java.util.Vector _hiddenColumnsList;
+
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Viewport()
+ {
+ super();
+ this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenColumnsList.addElement(vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenColumnsList.add(index, vHiddenColumns);
+ }
+
+ /**
+ */
+ public void deleteCentreColumnLabels()
+ {
+ this._has_centreColumnLabels = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected()
+ {
+ this._has_conservationSelected = false;
+ }
+
+ /**
+ */
+ public void deleteFollowHighlight()
+ {
+ this._has_followHighlight = false;
+ }
+
+ /**
+ */
+ public void deleteFollowSelection()
+ {
+ this._has_followSelection = false;
+ }
+
+ /**
+ */
+ public void deleteFontSize()
+ {
+ this._has_fontSize = false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle()
+ {
+ this._has_fontStyle = false;
+ }
+
+ /**
+ */
+ public void deleteGatheredViews()
+ {
+ this._has_gatheredViews = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
- /**
+ /**
*/
- public void deleteCentreColumnLabels(
- ) {
- this._has_centreColumnLabels= false;
- }
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteConservationSelected(
- ) {
- this._has_conservationSelected= false;
- }
-
- /**
- */
- public void deleteFollowHighlight(
- ) {
- this._has_followHighlight= false;
- }
-
- /**
- */
- public void deleteFollowSelection(
- ) {
- this._has_followSelection= false;
- }
-
- /**
- */
- public void deleteFontSize(
- ) {
- this._has_fontSize= false;
- }
-
- /**
- */
- public void deleteFontStyle(
- ) {
- this._has_fontStyle= false;
- }
-
- /**
- */
- public void deleteGatheredViews(
- ) {
- this._has_gatheredViews= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteIgnoreGapsinConsensus(
- ) {
- this._has_ignoreGapsinConsensus= false;
- }
-
- /**
- */
- public void deleteNormaliseSequenceLogo(
- ) {
- this._has_normaliseSequenceLogo= false;
- }
-
- /**
- */
- public void deletePidSelected(
- ) {
- this._has_pidSelected= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteRenderGaps(
- ) {
- this._has_renderGaps= false;
- }
+ public void deleteIgnoreGapsinConsensus()
+ {
+ this._has_ignoreGapsinConsensus = false;
+ }
- /**
+ /**
*/
- public void deleteRightAlignIds(
- ) {
- this._has_rightAlignIds= false;
- }
-
- /**
- */
- public void deleteScaleProteinAsCdna(
- ) {
- this._has_scaleProteinAsCdna= false;
- }
+ public void deleteNormaliseSequenceLogo()
+ {
+ this._has_normaliseSequenceLogo = false;
+ }
- /**
+ /**
*/
- public void deleteShowAnnotation(
- ) {
- this._has_showAnnotation= false;
- }
+ public void deletePidSelected()
+ {
+ this._has_pidSelected = false;
+ }
- /**
+ /**
*/
- public void deleteShowBoxes(
- ) {
- this._has_showBoxes= false;
- }
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
- /**
+ /**
*/
- public void deleteShowColourText(
- ) {
- this._has_showColourText= false;
- }
+ public void deleteRenderGaps()
+ {
+ this._has_renderGaps = false;
+ }
- /**
+ /**
*/
- public void deleteShowConsensusHistogram(
- ) {
- this._has_showConsensusHistogram= false;
- }
+ public void deleteRightAlignIds()
+ {
+ this._has_rightAlignIds = false;
+ }
- /**
+ /**
*/
- public void deleteShowDbRefTooltip(
- ) {
- this._has_showDbRefTooltip= false;
- }
+ public void deleteScaleProteinAsCdna()
+ {
+ this._has_scaleProteinAsCdna = false;
+ }
- /**
+ /**
*/
- public void deleteShowFullId(
- ) {
- this._has_showFullId= false;
- }
+ public void deleteShowAnnotation()
+ {
+ this._has_showAnnotation = false;
+ }
- /**
+ /**
*/
- public void deleteShowGroupConsensus(
- ) {
- this._has_showGroupConsensus= false;
- }
+ public void deleteShowBoxes()
+ {
+ this._has_showBoxes = false;
+ }
- /**
+ /**
*/
- public void deleteShowGroupConservation(
- ) {
- this._has_showGroupConservation= false;
- }
+ public void deleteShowColourText()
+ {
+ this._has_showColourText = false;
+ }
- /**
+ /**
*/
- public void deleteShowNPfeatureTooltip(
- ) {
- this._has_showNPfeatureTooltip= false;
- }
+ public void deleteShowConsensusHistogram()
+ {
+ this._has_showConsensusHistogram = false;
+ }
- /**
+ /**
*/
- public void deleteShowSequenceFeatures(
- ) {
- this._has_showSequenceFeatures= false;
- }
+ public void deleteShowDbRefTooltip()
+ {
+ this._has_showDbRefTooltip = false;
+ }
- /**
+ /**
*/
- public void deleteShowSequenceLogo(
- ) {
- this._has_showSequenceLogo= false;
- }
+ public void deleteShowFullId()
+ {
+ this._has_showFullId = false;
+ }
- /**
+ /**
*/
- public void deleteShowText(
- ) {
- this._has_showText= false;
- }
+ public void deleteShowGroupConsensus()
+ {
+ this._has_showGroupConsensus = false;
+ }
- /**
+ /**
*/
- public void deleteShowUnconserved(
- ) {
- this._has_showUnconserved= false;
- }
+ public void deleteShowGroupConservation()
+ {
+ this._has_showGroupConservation = false;
+ }
- /**
+ /**
*/
- public void deleteStartRes(
- ) {
- this._has_startRes= false;
- }
+ public void deleteShowNPfeatureTooltip()
+ {
+ this._has_showNPfeatureTooltip = false;
+ }
- /**
+ /**
*/
- public void deleteStartSeq(
- ) {
- this._has_startSeq= false;
- }
+ public void deleteShowSequenceFeatures()
+ {
+ this._has_showSequenceFeatures = false;
+ }
- /**
+ /**
*/
- public void deleteTextCol1(
- ) {
- this._has_textCol1= false;
- }
+ public void deleteShowSequenceLogo()
+ {
+ this._has_showSequenceLogo = false;
+ }
- /**
+ /**
*/
- public void deleteTextCol2(
- ) {
- this._has_textCol2= false;
- }
+ public void deleteShowText()
+ {
+ this._has_showText = false;
+ }
- /**
+ /**
*/
- public void deleteTextColThreshold(
- ) {
- this._has_textColThreshold= false;
- }
+ public void deleteShowUnconserved()
+ {
+ this._has_showUnconserved = false;
+ }
- /**
+ /**
*/
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteWrapAlignment(
- ) {
- this._has_wrapAlignment= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Method enumerateCalcIdParam.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.CalcIdParam elements
- */
- public java.util.Enumeration enumerateCalcIdParam(
- ) {
- return this._calcIdParamList.elements();
- }
-
- /**
- * Method enumerateHiddenColumns.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.HiddenColumns elements
- */
- public java.util.Enumeration enumerateHiddenColumns(
- ) {
- return this._hiddenColumnsList.elements();
- }
-
- /**
- * Returns the value of field 'annotationColours'.
- *
- * @return the value of field 'AnnotationColours'.
- */
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
- ) {
- return this._annotationColours;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour(
- ) {
- return this._bgColour;
- }
-
- /**
- * Method getCalcIdParam.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.CalcIdParam at the given index
- */
- public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size()) {
- throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
- }
-
- /**
- * Method getCalcIdParam.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
- ) {
- jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
- return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
- }
-
- /**
- * Method getCalcIdParamCount.
- *
- * @return the size of this collection
- */
- public int getCalcIdParamCount(
- ) {
- return this._calcIdParamList.size();
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean getCentreColumnLabels(
- ) {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'complementId'. The field
- * 'complementId' has the following description: The viewport
- * id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- *
- * @return the value of field 'ComplementId'.
- */
- public java.lang.String getComplementId(
- ) {
- return this._complementId;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean getFollowHighlight(
- ) {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean getFollowSelection(
- ) {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName(
- ) {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize(
- ) {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle(
- ) {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean getGatheredViews(
- ) {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Method getHiddenColumns.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.HiddenColumns at the given
- * index
- */
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size()) {
- throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
- }
-
- /**
- * Method getHiddenColumns.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
- ) {
- jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
- return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
- }
-
- /**
- * Method getHiddenColumnsCount.
- *
- * @return the size of this collection
- */
- public int getHiddenColumnsCount(
- ) {
- return this._hiddenColumnsList.size();
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean getIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean getNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean getRightAlignIds(
- ) {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'scaleProteinAsCdna'.
- *
- * @return the value of field 'ScaleProteinAsCdna'.
- */
- public boolean getScaleProteinAsCdna(
- ) {
- return this._scaleProteinAsCdna;
- }
-
- /**
- * Returns the value of field 'sequenceSetId'.
- *
- * @return the value of field 'SequenceSetId'.
- */
- public java.lang.String getSequenceSetId(
- ) {
- return this._sequenceSetId;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean getShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean getShowDbRefTooltip(
- ) {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean getShowGroupConsensus(
- ) {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean getShowGroupConservation(
- ) {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean getShowNPfeatureTooltip(
- ) {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean getShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean getShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes(
- ) {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq(
- ) {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return the value of field 'TextCol1'.
- */
- public int getTextCol1(
- ) {
- return this._textCol1;
- }
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return the value of field 'TextCol2'.
- */
- public int getTextCol2(
- ) {
- return this._textCol2;
- }
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return the value of field 'TextColThreshold'.
- */
- public int getTextColThreshold(
- ) {
- return this._textColThreshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewName'.
- *
- * @return the value of field 'ViewName'.
- */
- public java.lang.String getViewName(
- ) {
- return this._viewName;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasCentreColumnLabels.
- *
- * @return true if at least one CentreColumnLabels has been adde
- */
- public boolean hasCentreColumnLabels(
- ) {
- return this._has_centreColumnLabels;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been
- * added
- */
- public boolean hasConservationSelected(
- ) {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFollowHighlight.
- *
- * @return true if at least one FollowHighlight has been added
- */
- public boolean hasFollowHighlight(
- ) {
- return this._has_followHighlight;
- }
-
- /**
- * Method hasFollowSelection.
- *
- * @return true if at least one FollowSelection has been added
- */
- public boolean hasFollowSelection(
- ) {
- return this._has_followSelection;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize(
- ) {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle(
- ) {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasGatheredViews.
- *
- * @return true if at least one GatheredViews has been added
- */
- public boolean hasGatheredViews(
- ) {
- return this._has_gatheredViews;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasIgnoreGapsinConsensus.
- *
- * @return true if at least one IgnoreGapsinConsensus has been
- * added
- */
- public boolean hasIgnoreGapsinConsensus(
- ) {
- return this._has_ignoreGapsinConsensus;
- }
-
- /**
- * Method hasNormaliseSequenceLogo.
- *
- * @return true if at least one NormaliseSequenceLogo has been
- * added
- */
- public boolean hasNormaliseSequenceLogo(
- ) {
- return this._has_normaliseSequenceLogo;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected(
- ) {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps(
- ) {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasRightAlignIds.
- *
- * @return true if at least one RightAlignIds has been added
- */
- public boolean hasRightAlignIds(
- ) {
- return this._has_rightAlignIds;
- }
-
- /**
- * Method hasScaleProteinAsCdna.
- *
- * @return true if at least one ScaleProteinAsCdna has been adde
- */
- public boolean hasScaleProteinAsCdna(
- ) {
- return this._has_scaleProteinAsCdna;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation(
- ) {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes(
- ) {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText(
- ) {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConsensusHistogram.
- *
- * @return true if at least one ShowConsensusHistogram has been
- * added
- */
- public boolean hasShowConsensusHistogram(
- ) {
- return this._has_showConsensusHistogram;
- }
-
- /**
- * Method hasShowDbRefTooltip.
- *
- * @return true if at least one ShowDbRefTooltip has been added
- */
- public boolean hasShowDbRefTooltip(
- ) {
- return this._has_showDbRefTooltip;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId(
- ) {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowGroupConsensus.
- *
- * @return true if at least one ShowGroupConsensus has been adde
- */
- public boolean hasShowGroupConsensus(
- ) {
- return this._has_showGroupConsensus;
- }
-
- /**
- * Method hasShowGroupConservation.
- *
- * @return true if at least one ShowGroupConservation has been
- * added
- */
- public boolean hasShowGroupConservation(
- ) {
- return this._has_showGroupConservation;
- }
-
- /**
- * Method hasShowNPfeatureTooltip.
- *
- * @return true if at least one ShowNPfeatureTooltip has been
- * added
- */
- public boolean hasShowNPfeatureTooltip(
- ) {
- return this._has_showNPfeatureTooltip;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been
- * added
- */
- public boolean hasShowSequenceFeatures(
- ) {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowSequenceLogo.
- *
- * @return true if at least one ShowSequenceLogo has been added
- */
- public boolean hasShowSequenceLogo(
- ) {
- return this._has_showSequenceLogo;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText(
- ) {
- return this._has_showText;
- }
-
- /**
- * Method hasShowUnconserved.
- *
- * @return true if at least one ShowUnconserved has been added
- */
- public boolean hasShowUnconserved(
- ) {
- return this._has_showUnconserved;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes(
- ) {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq(
- ) {
- return this._has_startSeq;
- }
-
- /**
- * Method hasTextCol1.
- *
- * @return true if at least one TextCol1 has been added
- */
- public boolean hasTextCol1(
- ) {
- return this._has_textCol1;
- }
-
- /**
- * Method hasTextCol2.
- *
- * @return true if at least one TextCol2 has been added
- */
- public boolean hasTextCol2(
- ) {
- return this._has_textCol2;
- }
-
- /**
- * Method hasTextColThreshold.
- *
- * @return true if at least one TextColThreshold has been added
- */
- public boolean hasTextColThreshold(
- ) {
- return this._has_textColThreshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment(
- ) {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean isCentreColumnLabels(
- ) {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean isFollowHighlight(
- ) {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean isFollowSelection(
- ) {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean isGatheredViews(
- ) {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean isIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean isNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean isRightAlignIds(
- ) {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'scaleProteinAsCdna'.
- *
- * @return the value of field 'ScaleProteinAsCdna'.
- */
- public boolean isScaleProteinAsCdna(
- ) {
- return this._scaleProteinAsCdna;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean isShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean isShowDbRefTooltip(
- ) {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean isShowGroupConsensus(
- ) {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean isShowGroupConservation(
- ) {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean isShowNPfeatureTooltip(
- ) {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean isShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean isShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllCalcIdParam(
- ) {
- this._calcIdParamList.clear();
- }
-
- /**
- */
- public void removeAllHiddenColumns(
- ) {
- this._hiddenColumnsList.clear();
- }
-
- /**
- * Method removeCalcIdParam.
- *
- * @param vCalcIdParam
- * @return true if the object was removed from the collection.
- */
- public boolean removeCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
- boolean removed = _calcIdParamList.remove(vCalcIdParam);
- return removed;
- }
-
- /**
- * Method removeCalcIdParamAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
- final int index) {
- java.lang.Object obj = this._calcIdParamList.remove(index);
- return (jalview.schemabinding.version2.CalcIdParam) obj;
- }
-
- /**
- * Method removeHiddenColumns.
- *
- * @param vHiddenColumns
- * @return true if the object was removed from the collection.
- */
- public boolean removeHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
- boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
- return removed;
- }
-
- /**
- * Method removeHiddenColumnsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
- final int index) {
- java.lang.Object obj = this._hiddenColumnsList.remove(index);
- return (jalview.schemabinding.version2.HiddenColumns) obj;
- }
-
- /**
- * Sets the value of field 'annotationColours'.
- *
- * @param annotationColours the value of field
- * 'annotationColours'.
- */
- public void setAnnotationColours(
- final jalview.schemabinding.version2.AnnotationColours annotationColours) {
- this._annotationColours = annotationColours;
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour the value of field 'bgColour'.
- */
- public void setBgColour(
- final java.lang.String bgColour) {
- this._bgColour = bgColour;
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setCalcIdParam(
- final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size()) {
- throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
- }
-
- this._calcIdParamList.set(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vCalcIdParamArray
- */
- public void setCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
- //-- copy array
- _calcIdParamList.clear();
-
- for (int i = 0; i < vCalcIdParamArray.length; i++) {
- this._calcIdParamList.add(vCalcIdParamArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'centreColumnLabels'.
- *
- * @param centreColumnLabels the value of field
- * 'centreColumnLabels'.
- */
- public void setCentreColumnLabels(
- final boolean centreColumnLabels) {
- this._centreColumnLabels = centreColumnLabels;
- this._has_centreColumnLabels = true;
- }
-
- /**
- * Sets the value of field 'complementId'. The field
- * 'complementId' has the following description: The viewport
- * id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- *
- * @param complementId the value of field 'complementId'.
- */
- public void setComplementId(
- final java.lang.String complementId) {
- this._complementId = complementId;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected the value of field
- * 'conservationSelected'.
- */
- public void setConservationSelected(
- final boolean conservationSelected) {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'followHighlight'.
- *
- * @param followHighlight the value of field 'followHighlight'.
- */
- public void setFollowHighlight(
- final boolean followHighlight) {
- this._followHighlight = followHighlight;
- this._has_followHighlight = true;
- }
-
- /**
- * Sets the value of field 'followSelection'.
- *
- * @param followSelection the value of field 'followSelection'.
- */
- public void setFollowSelection(
- final boolean followSelection) {
- this._followSelection = followSelection;
- this._has_followSelection = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(
- final java.lang.String fontName) {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(
- final int fontSize) {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(
- final int fontStyle) {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'gatheredViews'.
- *
- * @param gatheredViews the value of field 'gatheredViews'.
- */
- public void setGatheredViews(
- final boolean gatheredViews) {
- this._gatheredViews = gatheredViews;
- this._has_gatheredViews = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setHiddenColumns(
- final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size()) {
- throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
- }
-
- this._hiddenColumnsList.set(index, vHiddenColumns);
- }
-
- /**
- *
- *
- * @param vHiddenColumnsArray
- */
- public void setHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
- //-- copy array
- _hiddenColumnsList.clear();
-
- for (int i = 0; i < vHiddenColumnsArray.length; i++) {
- this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'ignoreGapsinConsensus'.
- *
- * @param ignoreGapsinConsensus the value of field
- * 'ignoreGapsinConsensus'.
- */
- public void setIgnoreGapsinConsensus(
- final boolean ignoreGapsinConsensus) {
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;
- this._has_ignoreGapsinConsensus = true;
- }
-
- /**
- * Sets the value of field 'normaliseSequenceLogo'.
- *
- * @param normaliseSequenceLogo the value of field
- * 'normaliseSequenceLogo'.
- */
- public void setNormaliseSequenceLogo(
- final boolean normaliseSequenceLogo) {
- this._normaliseSequenceLogo = normaliseSequenceLogo;
- this._has_normaliseSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected the value of field 'pidSelected'.
- */
- public void setPidSelected(
- final boolean pidSelected) {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps the value of field 'renderGaps'.
- */
- public void setRenderGaps(
- final boolean renderGaps) {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'rightAlignIds'.
- *
- * @param rightAlignIds the value of field 'rightAlignIds'.
- */
- public void setRightAlignIds(
- final boolean rightAlignIds) {
- this._rightAlignIds = rightAlignIds;
- this._has_rightAlignIds = true;
- }
-
- /**
- * Sets the value of field 'scaleProteinAsCdna'.
- *
- * @param scaleProteinAsCdna the value of field
- * 'scaleProteinAsCdna'.
- */
- public void setScaleProteinAsCdna(
- final boolean scaleProteinAsCdna) {
- this._scaleProteinAsCdna = scaleProteinAsCdna;
- this._has_scaleProteinAsCdna = true;
- }
-
- /**
- * Sets the value of field 'sequenceSetId'.
- *
- * @param sequenceSetId the value of field 'sequenceSetId'.
- */
- public void setSequenceSetId(
- final java.lang.String sequenceSetId) {
- this._sequenceSetId = sequenceSetId;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(
- final boolean showAnnotation) {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes the value of field 'showBoxes'.
- */
- public void setShowBoxes(
- final boolean showBoxes) {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText the value of field 'showColourText'.
- */
- public void setShowColourText(
- final boolean showColourText) {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConsensusHistogram'.
- *
- * @param showConsensusHistogram the value of field
- * 'showConsensusHistogram'.
- */
- public void setShowConsensusHistogram(
- final boolean showConsensusHistogram) {
- this._showConsensusHistogram = showConsensusHistogram;
- this._has_showConsensusHistogram = true;
- }
-
- /**
- * Sets the value of field 'showDbRefTooltip'.
- *
- * @param showDbRefTooltip the value of field 'showDbRefTooltip'
- */
- public void setShowDbRefTooltip(
- final boolean showDbRefTooltip) {
- this._showDbRefTooltip = showDbRefTooltip;
- this._has_showDbRefTooltip = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId the value of field 'showFullId'.
- */
- public void setShowFullId(
- final boolean showFullId) {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showGroupConsensus'.
- *
- * @param showGroupConsensus the value of field
- * 'showGroupConsensus'.
- */
- public void setShowGroupConsensus(
- final boolean showGroupConsensus) {
- this._showGroupConsensus = showGroupConsensus;
- this._has_showGroupConsensus = true;
- }
-
- /**
- * Sets the value of field 'showGroupConservation'.
- *
- * @param showGroupConservation the value of field
- * 'showGroupConservation'.
- */
- public void setShowGroupConservation(
- final boolean showGroupConservation) {
- this._showGroupConservation = showGroupConservation;
- this._has_showGroupConservation = true;
- }
-
- /**
- * Sets the value of field 'showNPfeatureTooltip'.
- *
- * @param showNPfeatureTooltip the value of field
- * 'showNPfeatureTooltip'.
- */
- public void setShowNPfeatureTooltip(
- final boolean showNPfeatureTooltip) {
- this._showNPfeatureTooltip = showNPfeatureTooltip;
- this._has_showNPfeatureTooltip = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures the value of field
- * 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(
- final boolean showSequenceFeatures) {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showSequenceLogo'.
- *
- * @param showSequenceLogo the value of field 'showSequenceLogo'
- */
- public void setShowSequenceLogo(
- final boolean showSequenceLogo) {
- this._showSequenceLogo = showSequenceLogo;
- this._has_showSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText the value of field 'showText'.
- */
- public void setShowText(
- final boolean showText) {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'showUnconserved'.
- *
- * @param showUnconserved the value of field 'showUnconserved'.
- */
- public void setShowUnconserved(
- final boolean showUnconserved) {
- this._showUnconserved = showUnconserved;
- this._has_showUnconserved = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes the value of field 'startRes'.
- */
- public void setStartRes(
- final int startRes) {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq the value of field 'startSeq'.
- */
- public void setStartSeq(
- final int startSeq) {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1 the value of field 'textCol1'.
- */
- public void setTextCol1(
- final int textCol1) {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- }
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2 the value of field 'textCol2'.
- */
- public void setTextCol2(
- final int textCol2) {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- }
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold the value of field 'textColThreshold'
- */
- public void setTextColThreshold(
- final int textColThreshold) {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewName'.
- *
- * @param viewName the value of field 'viewName'.
- */
- public void setViewName(
- final java.lang.String viewName) {
- this._viewName = viewName;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(
- final boolean wrapAlignment) {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Viewport
- */
- public static jalview.schemabinding.version2.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ public void deleteStartRes()
+ {
+ this._has_startRes = false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq()
+ {
+ this._has_startSeq = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1()
+ {
+ this._has_textCol1 = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2()
+ {
+ this._has_textCol2 = false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold()
+ {
+ this._has_textColThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment()
+ {
+ this._has_wrapAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Method enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
+ * elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam()
+ {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
+ * Method enumerateHiddenColumns.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.HiddenColumns elements
+ */
+ public java.util.Enumeration enumerateHiddenColumns()
+ {
+ return this._hiddenColumnsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour()
+ {
+ return this._bgColour;
+ }
+
+ /**
+ * Method getCalcIdParam.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
+ * given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
+ .get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
+ {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
+ .toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount()
+ {
+ return this._calcIdParamList.size();
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean getCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'complementId'. The field 'complementId' has the
+ * following description: The viewport id of this viewport's (cdna/protein)
+ * coding complement, if any
+ *
+ *
+ * @return the value of field 'ComplementId'.
+ */
+ public java.lang.String getComplementId()
+ {
+ return this._complementId;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean getFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean getFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean getGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Method getHiddenColumns.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.HiddenColumns at
+ * the given index
+ */
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
+ .get(index);
+ }
+
+ /**
+ * Method getHiddenColumns.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+ {
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
+ .toArray(array);
+ }
+
+ /**
+ * Method getHiddenColumnsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenColumnsCount()
+ {
+ return this._hiddenColumnsList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: unique id used by jalview to synchronize between stored and
+ * instantiated views
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean getRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean getScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSetId'.
+ *
+ * @return the value of field 'SequenceSetId'.
+ */
+ public java.lang.String getSequenceSetId()
+ {
+ return this._sequenceSetId;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean getShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean getShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean getShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean getShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes()
+ {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq()
+ {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1()
+ {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2()
+ {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold()
+ {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewName'.
+ *
+ * @return the value of field 'ViewName'.
+ */
+ public java.lang.String getViewName()
+ {
+ return this._viewName;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCentreColumnLabels.
+ *
+ * @return true if at least one CentreColumnLabels has been adde
+ */
+ public boolean hasCentreColumnLabels()
+ {
+ return this._has_centreColumnLabels;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been added
+ */
+ public boolean hasConservationSelected()
+ {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFollowHighlight.
+ *
+ * @return true if at least one FollowHighlight has been added
+ */
+ public boolean hasFollowHighlight()
+ {
+ return this._has_followHighlight;
+ }
+
+ /**
+ * Method hasFollowSelection.
+ *
+ * @return true if at least one FollowSelection has been added
+ */
+ public boolean hasFollowSelection()
+ {
+ return this._has_followSelection;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasGatheredViews.
+ *
+ * @return true if at least one GatheredViews has been added
+ */
+ public boolean hasGatheredViews()
+ {
+ return this._has_gatheredViews;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been added
+ */
+ public boolean hasIgnoreGapsinConsensus()
+ {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been added
+ */
+ public boolean hasNormaliseSequenceLogo()
+ {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected()
+ {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps()
+ {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasRightAlignIds.
+ *
+ * @return true if at least one RightAlignIds has been added
+ */
+ public boolean hasRightAlignIds()
+ {
+ return this._has_rightAlignIds;
+ }
+
+ /**
+ * Method hasScaleProteinAsCdna.
+ *
+ * @return true if at least one ScaleProteinAsCdna has been adde
+ */
+ public boolean hasScaleProteinAsCdna()
+ {
+ return this._has_scaleProteinAsCdna;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation()
+ {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes()
+ {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText()
+ {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been added
+ */
+ public boolean hasShowConsensusHistogram()
+ {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowDbRefTooltip.
+ *
+ * @return true if at least one ShowDbRefTooltip has been added
+ */
+ public boolean hasShowDbRefTooltip()
+ {
+ return this._has_showDbRefTooltip;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId()
+ {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowGroupConsensus.
+ *
+ * @return true if at least one ShowGroupConsensus has been adde
+ */
+ public boolean hasShowGroupConsensus()
+ {
+ return this._has_showGroupConsensus;
+ }
+
+ /**
+ * Method hasShowGroupConservation.
+ *
+ * @return true if at least one ShowGroupConservation has been added
+ */
+ public boolean hasShowGroupConservation()
+ {
+ return this._has_showGroupConservation;
+ }
+
+ /**
+ * Method hasShowNPfeatureTooltip.
+ *
+ * @return true if at least one ShowNPfeatureTooltip has been added
+ */
+ public boolean hasShowNPfeatureTooltip()
+ {
+ return this._has_showNPfeatureTooltip;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been added
+ */
+ public boolean hasShowSequenceFeatures()
+ {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo()
+ {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText()
+ {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved()
+ {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes()
+ {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq()
+ {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1()
+ {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2()
+ {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold()
+ {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment()
+ {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean isFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean isFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean isGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean isRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean isShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean isShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean isShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllCalcIdParam()
+ {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
+ public void removeAllHiddenColumns()
+ {
+ this._hiddenColumnsList.clear();
+ }
+
+ /**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index)
+ {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
+ * Method removeHiddenColumns.
+ *
+ * @param vHiddenColumns
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ {
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenColumnsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+ final int index)
+ {
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);
+ return (jalview.schemabinding.version2.HiddenColumns) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final java.lang.String bgColour)
+ {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
+ {
+ // -- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++)
+ {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'centreColumnLabels'.
+ *
+ * @param centreColumnLabels
+ * the value of field 'centreColumnLabels'.
+ */
+ public void setCentreColumnLabels(final boolean centreColumnLabels)
+ {
+ this._centreColumnLabels = centreColumnLabels;
+ this._has_centreColumnLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'complementId'. The field 'complementId' has the
+ * following description: The viewport id of this viewport's (cdna/protein)
+ * coding complement, if any
+ *
+ *
+ * @param complementId
+ * the value of field 'complementId'.
+ */
+ public void setComplementId(final java.lang.String complementId)
+ {
+ this._complementId = complementId;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected
+ * the value of field 'conservationSelected'.
+ */
+ public void setConservationSelected(final boolean conservationSelected)
+ {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'followHighlight'.
+ *
+ * @param followHighlight
+ * the value of field 'followHighlight'.
+ */
+ public void setFollowHighlight(final boolean followHighlight)
+ {
+ this._followHighlight = followHighlight;
+ this._has_followHighlight = true;
+ }
+
+ /**
+ * Sets the value of field 'followSelection'.
+ *
+ * @param followSelection
+ * the value of field 'followSelection'.
+ */
+ public void setFollowSelection(final boolean followSelection)
+ {
+ this._followSelection = followSelection;
+ this._has_followSelection = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'gatheredViews'.
+ *
+ * @param gatheredViews
+ * the value of field 'gatheredViews'.
+ */
+ public void setGatheredViews(final boolean gatheredViews)
+ {
+ this._gatheredViews = gatheredViews;
+ this._has_gatheredViews = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setHiddenColumns(final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ this._hiddenColumnsList.set(index, vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumnsArray
+ */
+ public void setHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
+ {
+ // -- copy array
+ _hiddenColumnsList.clear();
+
+ for (int i = 0; i < vHiddenColumnsArray.length; i++)
+ {
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus
+ * the value of field 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+ {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo
+ * the value of field 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+ {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected
+ * the value of field 'pidSelected'.
+ */
+ public void setPidSelected(final boolean pidSelected)
+ {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps
+ * the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(final boolean renderGaps)
+ {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'rightAlignIds'.
+ *
+ * @param rightAlignIds
+ * the value of field 'rightAlignIds'.
+ */
+ public void setRightAlignIds(final boolean rightAlignIds)
+ {
+ this._rightAlignIds = rightAlignIds;
+ this._has_rightAlignIds = true;
+ }
+
+ /**
+ * Sets the value of field 'scaleProteinAsCdna'.
+ *
+ * @param scaleProteinAsCdna
+ * the value of field 'scaleProteinAsCdna'.
+ */
+ public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
+ {
+ this._scaleProteinAsCdna = scaleProteinAsCdna;
+ this._has_scaleProteinAsCdna = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSetId'.
+ *
+ * @param sequenceSetId
+ * the value of field 'sequenceSetId'.
+ */
+ public void setSequenceSetId(final java.lang.String sequenceSetId)
+ {
+ this._sequenceSetId = sequenceSetId;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation
+ * the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(final boolean showAnnotation)
+ {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes
+ * the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(final boolean showBoxes)
+ {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText
+ * the value of field 'showColourText'.
+ */
+ public void setShowColourText(final boolean showColourText)
+ {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram
+ * the value of field 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+ {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showDbRefTooltip'.
+ *
+ * @param showDbRefTooltip
+ * the value of field 'showDbRefTooltip'
+ */
+ public void setShowDbRefTooltip(final boolean showDbRefTooltip)
+ {
+ this._showDbRefTooltip = showDbRefTooltip;
+ this._has_showDbRefTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId
+ * the value of field 'showFullId'.
+ */
+ public void setShowFullId(final boolean showFullId)
+ {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConsensus'.
+ *
+ * @param showGroupConsensus
+ * the value of field 'showGroupConsensus'.
+ */
+ public void setShowGroupConsensus(final boolean showGroupConsensus)
+ {
+ this._showGroupConsensus = showGroupConsensus;
+ this._has_showGroupConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConservation'.
+ *
+ * @param showGroupConservation
+ * the value of field 'showGroupConservation'.
+ */
+ public void setShowGroupConservation(final boolean showGroupConservation)
+ {
+ this._showGroupConservation = showGroupConservation;
+ this._has_showGroupConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showNPfeatureTooltip'.
+ *
+ * @param showNPfeatureTooltip
+ * the value of field 'showNPfeatureTooltip'.
+ */
+ public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
+ {
+ this._showNPfeatureTooltip = showNPfeatureTooltip;
+ this._has_showNPfeatureTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures
+ * the value of field 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+ {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo
+ * the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(final boolean showSequenceLogo)
+ {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText
+ * the value of field 'showText'.
+ */
+ public void setShowText(final boolean showText)
+ {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved
+ * the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(final boolean showUnconserved)
+ {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes
+ * the value of field 'startRes'.
+ */
+ public void setStartRes(final int startRes)
+ {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq
+ * the value of field 'startSeq'.
+ */
+ public void setStartSeq(final int startSeq)
+ {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1
+ * the value of field 'textCol1'.
+ */
+ public void setTextCol1(final int textCol1)
+ {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2
+ * the value of field 'textCol2'.
+ */
+ public void setTextCol2(final int textCol2)
+ {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold
+ * the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(final int textColThreshold)
+ {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewName'.
+ *
+ * @param viewName
+ * the value of field 'viewName'.
+ */
+ public void setViewName(final java.lang.String viewName)
+ {
+ this._viewName = viewName;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment
+ * the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(final boolean wrapAlignment)
+ {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Viewport
+ */
+ public static jalview.schemabinding.version2.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Viewport.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class WebServiceParameterSet implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * The short name for the parameter set. This will be shown
- * amongst the
- * other presets for the web service.
- *
- */
- private java.lang.String _name;
-
- /**
- * A Jalview Web Service Parameter Set container
- * version number.
- * Version 1 created for storing Jaba user presets.
- *
- */
- private java.lang.String _version;
-
- /**
- * Short description - as utf8 encoded text. This is
- * usually displayed
- * in the body of an HTML capable tooltip, so HTML tags may be
- * embedded
- * using standard UTF8 encoding.
- *
- */
- private java.lang.String _description;
-
- /**
- * URL for which the parameter set is valid. Jalview will use
- * it to
- * match up parameter sets to service instances that can parse
- * the
- * parameter set payload.
- *
- */
- private java.util.Vector _serviceURLList;
-
- /**
- * UTF8 encoded string to be processed into a specific web
- * services'
- * parameter set. Note - newlines may be important to the
- * structure
- * of this file.
- *
- */
- private java.lang.String _parameters;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public WebServiceParameterSet() {
- super();
- this._serviceURLList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addServiceURL(
- final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException {
- this._serviceURLList.addElement(vServiceURL);
+public class WebServiceParameterSet implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * The short name for the parameter set. This will be shown amongst the other
+ * presets for the web service.
+ *
+ */
+ private java.lang.String _name;
+
+ /**
+ * A Jalview Web Service Parameter Set container version number. Version 1
+ * created for storing Jaba user presets.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Short description - as utf8 encoded text. This is usually displayed in the
+ * body of an HTML capable tooltip, so HTML tags may be embedded using
+ * standard UTF8 encoding.
+ *
+ */
+ private java.lang.String _description;
+
+ /**
+ * URL for which the parameter set is valid. Jalview will use it to match up
+ * parameter sets to service instances that can parse the parameter set
+ * payload.
+ *
+ */
+ private java.util.Vector _serviceURLList;
+
+ /**
+ * UTF8 encoded string to be processed into a specific web services' parameter
+ * set. Note - newlines may be important to the structure of this file.
+ *
+ */
+ private java.lang.String _parameters;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public WebServiceParameterSet()
+ {
+ super();
+ this._serviceURLList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addServiceURL(final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._serviceURLList.addElement(vServiceURL);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addServiceURL(final int index,
+ final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._serviceURLList.add(index, vServiceURL);
+ }
+
+ /**
+ * Method enumerateServiceURL.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateServiceURL()
+ {
+ return this._serviceURLList.elements();
+ }
+
+ /**
+ * Returns the value of field 'description'. The field 'description' has the
+ * following description: Short description - as utf8 encoded text. This is
+ * usually displayed in the body of an HTML capable tooltip, so HTML tags may
+ * be embedded using standard UTF8 encoding.
+ *
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'name'. The field 'name' has the following
+ * description: The short name for the parameter set. This will be shown
+ * amongst the other presets for the web service.
+ *
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'parameters'. The field 'parameters' has the
+ * following description: UTF8 encoded string to be processed into a specific
+ * web services' parameter set. Note - newlines may be important to the
+ * structure of this file.
+ *
+ *
+ * @return the value of field 'Parameters'.
+ */
+ public java.lang.String getParameters()
+ {
+ return this._parameters;
+ }
+
+ /**
+ * Method getServiceURL.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getServiceURL(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._serviceURLList.size())
+ {
+ throw new IndexOutOfBoundsException("getServiceURL: Index value '"
+ + index + "' not in range [0.."
+ + (this._serviceURLList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addServiceURL(
- final int index,
- final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException {
- this._serviceURLList.add(index, vServiceURL);
+ return (java.lang.String) _serviceURLList.get(index);
+ }
+
+ /**
+ * Method getServiceURL.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getServiceURL()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._serviceURLList.toArray(array);
+ }
+
+ /**
+ * Method getServiceURLCount.
+ *
+ * @return the size of this collection
+ */
+ public int getServiceURLCount()
+ {
+ return this._serviceURLList.size();
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: A Jalview Web Service Parameter Set container version number.
+ * Version 1 created for storing Jaba user presets.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- * Method enumerateServiceURL.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateServiceURL(
- ) {
- return this._serviceURLList.elements();
- }
-
- /**
- * Returns the value of field 'description'. The field
- * 'description' has the following description: Short
- * description - as utf8 encoded text. This is
- * usually displayed
- * in the body of an HTML capable tooltip, so HTML tags may be
- * embedded
- * using standard UTF8 encoding.
- *
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'name'. The field 'name' has the
- * following description: The short name for the parameter set.
- * This will be shown amongst the
- * other presets for the web service.
- *
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'parameters'. The field
- * 'parameters' has the following description: UTF8 encoded
- * string to be processed into a specific web services'
- * parameter set. Note - newlines may be important to the
- * structure
- * of this file.
- *
- *
- * @return the value of field 'Parameters'.
- */
- public java.lang.String getParameters(
- ) {
- return this._parameters;
- }
-
- /**
- * Method getServiceURL.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getServiceURL(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._serviceURLList.size()) {
- throw new IndexOutOfBoundsException("getServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
- }
-
- return (java.lang.String) _serviceURLList.get(index);
- }
-
- /**
- * Method getServiceURL.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getServiceURL(
- ) {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._serviceURLList.toArray(array);
- }
-
- /**
- * Method getServiceURLCount.
- *
- * @return the size of this collection
- */
- public int getServiceURLCount(
- ) {
- return this._serviceURLList.size();
- }
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: A Jalview Web Service
- * Parameter Set container
- * version number.
- * Version 1 created for storing Jaba user presets.
- *
- *
- * @return the value of field 'Version'.
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public java.lang.String getVersion(
- ) {
- return this._version;
+ public void removeAllServiceURL()
+ {
+ this._serviceURLList.clear();
+ }
+
+ /**
+ * Method removeServiceURL.
+ *
+ * @param vServiceURL
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeServiceURL(final java.lang.String vServiceURL)
+ {
+ boolean removed = _serviceURLList.remove(vServiceURL);
+ return removed;
+ }
+
+ /**
+ * Method removeServiceURLAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeServiceURLAt(final int index)
+ {
+ java.lang.Object obj = this._serviceURLList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ * Sets the value of field 'description'. The field 'description' has the
+ * following description: Short description - as utf8 encoded text. This is
+ * usually displayed in the body of an HTML capable tooltip, so HTML tags may
+ * be embedded using standard UTF8 encoding.
+ *
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'name'. The field 'name' has the following
+ * description: The short name for the parameter set. This will be shown
+ * amongst the other presets for the web service.
+ *
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'parameters'. The field 'parameters' has the
+ * following description: UTF8 encoded string to be processed into a specific
+ * web services' parameter set. Note - newlines may be important to the
+ * structure of this file.
+ *
+ *
+ * @param parameters
+ * the value of field 'parameters'.
+ */
+ public void setParameters(final java.lang.String parameters)
+ {
+ this._parameters = parameters;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setServiceURL(final int index,
+ final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._serviceURLList.size())
+ {
+ throw new IndexOutOfBoundsException("setServiceURL: Index value '"
+ + index + "' not in range [0.."
+ + (this._serviceURLList.size() - 1) + "]");
}
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllServiceURL(
- ) {
- this._serviceURLList.clear();
- }
-
- /**
- * Method removeServiceURL.
- *
- * @param vServiceURL
- * @return true if the object was removed from the collection.
- */
- public boolean removeServiceURL(
- final java.lang.String vServiceURL) {
- boolean removed = _serviceURLList.remove(vServiceURL);
- return removed;
- }
-
- /**
- * Method removeServiceURLAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeServiceURLAt(
- final int index) {
- java.lang.Object obj = this._serviceURLList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- * Sets the value of field 'description'. The field
- * 'description' has the following description: Short
- * description - as utf8 encoded text. This is
- * usually displayed
- * in the body of an HTML capable tooltip, so HTML tags may be
- * embedded
- * using standard UTF8 encoding.
- *
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'name'. The field 'name' has the
- * following description: The short name for the parameter set.
- * This will be shown amongst the
- * other presets for the web service.
- *
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'parameters'. The field 'parameters'
- * has the following description: UTF8 encoded string to be
- * processed into a specific web services'
- * parameter set. Note - newlines may be important to the
- * structure
- * of this file.
- *
- *
- * @param parameters the value of field 'parameters'.
- */
- public void setParameters(
- final java.lang.String parameters) {
- this._parameters = parameters;
- }
-
- /**
- *
- *
- * @param index
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setServiceURL(
- final int index,
- final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._serviceURLList.size()) {
- throw new IndexOutOfBoundsException("setServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
- }
-
- this._serviceURLList.set(index, vServiceURL);
- }
-
- /**
- *
- *
- * @param vServiceURLArray
- */
- public void setServiceURL(
- final java.lang.String[] vServiceURLArray) {
- //-- copy array
- _serviceURLList.clear();
-
- for (int i = 0; i < vServiceURLArray.length; i++) {
- this._serviceURLList.add(vServiceURLArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: A Jalview Web Service Parameter
- * Set container
- * version number.
- * Version 1 created for storing Jaba user presets.
- *
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.WebServiceParameterSet
- */
- public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.WebServiceParameterSet.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._serviceURLList.set(index, vServiceURL);
+ }
+
+ /**
+ *
+ *
+ * @param vServiceURLArray
+ */
+ public void setServiceURL(final java.lang.String[] vServiceURLArray)
+ {
+ // -- copy array
+ _serviceURLList.clear();
+
+ for (int i = 0; i < vServiceURLArray.length; i++)
+ {
+ this._serviceURLList.add(vServiceURLArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: A Jalview Web Service Parameter Set container version number.
+ * Version 1 created for storing Jaba user presets.
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.WebServiceParameterSet
+ */
+ public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.WebServiceParameterSet.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AlcodMap;
*
* @version $Revision$ $Date$
*/
-public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlcodMapDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "alcodMap";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _dnasq
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlcodMap target = (AlcodMap) object;
- return target.getDnasq();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlcodMap target = (AlcodMap) object;
- target.setDnasq( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dnasq
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _mapping
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlcodMap target = (AlcodMap) object;
- return target.getMapping();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlcodMap target = (AlcodMap) object;
- target.setMapping( (jalview.schemabinding.version2.Mapping) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Mapping();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapping
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
+public class AlcodMapDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlcodMapDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "alcodMap";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _dnasq
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_dnasq", "dnasq",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AlcodMap target = (AlcodMap) object;
+ return target.getDnasq();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AlcodMap target = (AlcodMap) object;
+ target.setDnasq((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _dnasq
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AlcodMap.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _mapping
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Mapping.class, "_mapping",
+ "Mapping", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AlcodMap target = (AlcodMap) object;
+ return target.getMapping();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AlcodMap target = (AlcodMap) object;
+ target.setMapping((jalview.schemabinding.version2.Mapping) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Mapping();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _mapping
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AlcodMap.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Alcodon;
*
* @version $Revision$ $Date$
*/
-public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlcodonDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "alcodon";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _pos1
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alcodon target = (Alcodon) object;
- if (!target.hasPos1()) { return null; }
- return new java.lang.Long(target.getPos1());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alcodon target = (Alcodon) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePos1();
- return;
- }
- target.setPos1( ((java.lang.Long) value).longValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pos1
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.LongValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _pos2
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alcodon target = (Alcodon) object;
- if (!target.hasPos2()) { return null; }
- return new java.lang.Long(target.getPos2());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alcodon target = (Alcodon) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePos2();
- return;
- }
- target.setPos2( ((java.lang.Long) value).longValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pos2
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.LongValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();
- fieldValidator.setValidator(typeValidator);
+public class AlcodonDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlcodonDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "alcodon";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _pos1
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Long.TYPE, "_pos1", "pos1",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Alcodon target = (Alcodon) object;
+ if (!target.hasPos1())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _pos3
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alcodon target = (Alcodon) object;
- if (!target.hasPos3()) { return null; }
- return new java.lang.Long(target.getPos3());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alcodon target = (Alcodon) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePos3();
- return;
- }
- target.setPos3( ((java.lang.Long) value).longValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pos3
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.LongValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Long(target.getPos1());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Alcodon target = (Alcodon) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePos1();
+ return;
+ }
+ target.setPos1(((java.lang.Long) value).longValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+ // -- validation code for: _pos1
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.LongValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pos2
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Long.TYPE, "_pos2", "pos2",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Alcodon target = (Alcodon) object;
+ if (!target.hasPos2())
+ {
+ return null;
+ }
+ return new java.lang.Long(target.getPos2());
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Alcodon target = (Alcodon) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePos2();
+ return;
+ }
+ target.setPos2(((java.lang.Long) value).longValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _pos2
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.LongValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _pos3
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Long.TYPE, "_pos3", "pos3",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Alcodon target = (Alcodon) object;
+ if (!target.hasPos3())
+ {
+ return null;
+ }
+ return new java.lang.Long(target.getPos3());
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Alcodon.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Alcodon target = (Alcodon) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePos3();
+ return;
+ }
+ target.setPos3(((java.lang.Long) value).longValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _pos3
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.LongValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Alcodon.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AlcodonFrame;
*
* @version $Revision$ $Date$
*/
-public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlcodonFrameDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "AlcodonFrame";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _alcodonList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlcodonFrame target = (AlcodonFrame) object;
- return target.getAlcodon();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlcodonFrame target = (AlcodonFrame) object;
- target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- AlcodonFrame target = (AlcodonFrame) object;
- target.removeAllAlcodon();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Alcodon();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alcodonList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class AlcodonFrameDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlcodonFrameDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "AlcodonFrame";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _alcodonList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Alcodon.class, "_alcodonList",
+ "alcodon", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ return target.getAlcodon();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ target.addAlcodon((jalview.schemabinding.version2.Alcodon) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _alcodMapList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlcodonFrame target = (AlcodonFrame) object;
- return target.getAlcodMap();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlcodonFrame target = (AlcodonFrame) object;
- target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- AlcodonFrame target = (AlcodonFrame) object;
- target.removeAllAlcodMap();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.AlcodMap();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alcodMapList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ target.removeAllAlcodon();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Alcodon();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _alcodonList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _alcodMapList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList",
+ "alcodMap", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ return target.getAlcodMap();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ target.addAlcodMap((jalview.schemabinding.version2.AlcodMap) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ AlcodonFrame target = (AlcodonFrame) object;
+ target.removeAllAlcodMap();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AlcodMap();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _alcodMapList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AlcodonFrame.class;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AlcodonFrame.class;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AnnotationColourScheme;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColourSchemeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColourSchemeDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "AnnotationColourScheme";
- _elementDefinition = false;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _aboveThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasAboveThreshold()) { return null; }
- return new java.lang.Integer(target.getAboveThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAboveThreshold();
- return;
- }
- target.setAboveThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _aboveThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _annotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- return target.getAnnotation();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- target.setAnnotation( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class AnnotationColourSchemeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourSchemeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColourScheme";
+ _elementDefinition = false;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _aboveThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasAboveThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _minColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasMinColour()) { return null; }
- return new java.lang.Integer(target.getMinColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMinColour();
- return;
- }
- target.setMinColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _minColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getAboveThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAboveThreshold();
+ return;
+ }
+ target.setAboveThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _maxColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasMaxColour()) { return null; }
- return new java.lang.Integer(target.getMaxColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMaxColour();
- return;
- }
- target.setMaxColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _maxColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _aboveThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _annotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_annotation", "annotation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getAnnotation();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setAnnotation((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colourScheme
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- return target.getColourScheme();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- target.setColourScheme( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourScheme
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _minColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_minColour", "minColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMinColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasThreshold()) { return null; }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshold();
- return;
- }
- target.setThreshold( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ return new java.lang.Integer(target.getMinColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMinColour();
+ return;
+ }
+ target.setMinColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _perSequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasPerSequence()) { return null; }
- return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePerSequence();
- return;
- }
- target.setPerSequence( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _perSequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _minColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _maxColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_maxColour", "maxColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMaxColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _predefinedColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- if (!target.hasPredefinedColours()) { return null; }
- return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColourScheme target = (AnnotationColourScheme) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePredefinedColours();
- return;
- }
- target.setPredefinedColours( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _predefinedColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getMaxColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMaxColour();
+ return;
+ }
+ target.setMaxColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _maxColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourScheme
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_colourScheme", "colourScheme",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getColourScheme();
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setColourScheme((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _colourScheme
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getThreshold());
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AnnotationColourScheme.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ // -- _perSequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_perSequence", "perSequence",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPerSequence())
+ {
+ return null;
+ }
+ return (target.getPerSequence() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePerSequence();
+ return;
+ }
+ target.setPerSequence(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _perSequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _predefinedColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_predefinedColours",
+ "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPredefinedColours())
+ {
+ return null;
+ }
+ return (target.getPredefinedColours() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePredefinedColours();
+ return;
+ }
+ target.setPredefinedColours(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _predefinedColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationColourScheme.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import jalview.schemabinding.version2.AnnotationColours;
/**
* Class AnnotationColoursDescriptor.
*
* @version $Revision$ $Date$
*/
-public class AnnotationColoursDescriptor extends jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColoursDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "AnnotationColours";
- _elementDefinition = true;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AnnotationColours.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+public class AnnotationColoursDescriptor
+ extends
+ jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColoursDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColours";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationColours.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Annotation;
*
* @version $Revision$ $Date$
*/
-public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "Annotation";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _graph
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasGraph()) { return null; }
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setGraph( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graph
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+public class AnnotationDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "Annotation";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _graph
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_graph", "graph",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasGraph())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _graphType
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasGraphType()) { return null; }
- return new java.lang.Integer(target.getGraphType());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGraphType();
- return;
- }
- target.setGraphType( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graphType
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getGraph() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setGraph(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _sequenceRef
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getSequenceRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setSequenceRef( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceRef
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _graph
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _graphType
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_graphType", "graphType",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasGraphType())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _groupRef
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getGroupRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setGroupRef( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _groupRef
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getGraphType());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGraphType();
+ return;
+ }
+ target.setGraphType(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _graphColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasGraphColour()) { return null; }
- return new java.lang.Integer(target.getGraphColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGraphColour();
- return;
- }
- target.setGraphColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graphColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _graphType
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _sequenceRef
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_sequenceRef", "sequenceRef",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getSequenceRef();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setSequenceRef((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _graphGroup
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasGraphGroup()) { return null; }
- return new java.lang.Integer(target.getGraphGroup());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGraphGroup();
- return;
- }
- target.setGraphGroup( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graphGroup
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequenceRef
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _groupRef
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_groupRef", "groupRef",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getGroupRef();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setGroupRef((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _graphHeight
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphHeight", "graphHeight", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasGraphHeight()) { return null; }
- return new java.lang.Integer(target.getGraphHeight());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGraphHeight();
- return;
- }
- target.setGraphHeight( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graphHeight
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _groupRef
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _graphColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_graphColour", "graphColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasGraphColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getGraphColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGraphColour();
+ return;
+ }
+ target.setGraphColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _scoreOnly
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasScoreOnly()) { return null; }
- return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteScoreOnly();
- return;
- }
- target.setScoreOnly( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _scoreOnly
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _graphColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _graphGroup
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasGraphGroup())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _score
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasScore()) { return null; }
- return new java.lang.Double(target.getScore());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteScore();
- return;
- }
- target.setScore( ((java.lang.Double) value).doubleValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _score
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.DoubleValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-1.7976931348623157E308);
- typeValidator.setMaxInclusive(1.7976931348623157E308);
+ return new java.lang.Integer(target.getGraphGroup());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGraphGroup();
+ return;
+ }
+ target.setGraphGroup(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _visible
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasVisible()) { return null; }
- return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteVisible();
- return;
- }
- target.setVisible( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _visible
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _graphGroup
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _graphHeight
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_graphHeight", "graphHeight",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasGraphHeight())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _centreColLabels
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasCentreColLabels()) { return null; }
- return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteCentreColLabels();
- return;
- }
- target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _centreColLabels
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getGraphHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGraphHeight();
+ return;
+ }
+ target.setGraphHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _scaleColLabels
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasScaleColLabels()) { return null; }
- return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteScaleColLabels();
- return;
- }
- target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _scaleColLabels
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _graphHeight
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _showAllColLabels
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasShowAllColLabels()) { return null; }
- return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowAllColLabels();
- return;
- }
- target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showAllColLabels
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scoreOnly
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasScoreOnly())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _autoCalculated
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasAutoCalculated()) { return null; }
- return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAutoCalculated();
- return;
- }
- target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _autoCalculated
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getScoreOnly() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScoreOnly();
+ return;
+ }
+ target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _belowAlignment
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- if (!target.hasBelowAlignment()) { return null; }
- return (target.getBelowAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteBelowAlignment();
- return;
- }
- target.setBelowAlignment( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _belowAlignment
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scoreOnly
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _score
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Double.TYPE, "_score", "score",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasScore())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _calcId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_calcId", "calcId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getCalcId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setCalcId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _calcId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Double(target.getScore());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScore();
+ return;
+ }
+ target.setScore(((java.lang.Double) value).doubleValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _annotationElementList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getAnnotationElement();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Annotation target = (Annotation) object;
- target.removeAllAnnotationElement();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.AnnotationElement();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationElementList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _score
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.DoubleValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-1.7976931348623157E308);
+ typeValidator.setMaxInclusive(1.7976931348623157E308);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _visible
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_visible", "visible",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasVisible())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _label
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getLabel();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setLabel( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _label
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return (target.getVisible() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteVisible();
+ return;
+ }
+ target.setVisible(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setDescription( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _visible
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _centreColLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasCentreColLabels())
+ {
+ return null;
+ }
+ return (target.getCentreColLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteCentreColLabels();
+ return;
+ }
+ target.setCentreColLabels(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _thresholdLine
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getThresholdLine();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.ThresholdLine();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _thresholdLine
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _centreColLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scaleColLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasScaleColLabels())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Annotation target = (Annotation) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Annotation target = (Annotation) object;
- target.addProperty( (jalview.schemabinding.version2.Property) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Annotation target = (Annotation) object;
- target.removeAllProperty();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ return (target.getScaleColLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScaleColLabels();
+ return;
+ }
+ target.setScaleColLabels(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scaleColLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _showAllColLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showAllColLabels",
+ "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasShowAllColLabels())
+ {
+ return null;
+ }
+ return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowAllColLabels();
+ return;
+ }
+ target.setShowAllColLabels(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ // -- validation code for: _showAllColLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _autoCalculated
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasAutoCalculated())
+ {
+ return null;
+ }
+ return (target.getAutoCalculated() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAutoCalculated();
+ return;
+ }
+ target.setAutoCalculated(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _autoCalculated
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _belowAlignment
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ if (!target.hasBelowAlignment())
+ {
+ return null;
+ }
+ return (target.getBelowAlignment() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteBelowAlignment();
+ return;
+ }
+ target.setBelowAlignment(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _belowAlignment
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _calcId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_calcId", "calcId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getCalcId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setCalcId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Annotation.class;
+ // -- validation code for: _calcId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
+ // -- _annotationElementList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AnnotationElement.class,
+ "_annotationElementList", "annotationElement",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getAnnotationElement();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.removeAllAnnotationElement();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AnnotationElement();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationElementList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _label
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_label", "label",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getLabel();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setLabel((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _label
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_description", "description",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getDescription();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setDescription((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _thresholdLine
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.ThresholdLine.class,
+ "_thresholdLine", "thresholdLine",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getThresholdLine();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.ThresholdLine();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _thresholdLine
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Property.class, "_propertyList",
+ "property", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Annotation target = (Annotation) object;
+ return target.getProperty();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.addProperty((jalview.schemabinding.version2.Property) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Annotation target = (Annotation) object;
+ target.removeAllProperty();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Annotation.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AnnotationElement;
*
* @version $Revision$ $Date$
*/
-public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElementDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "annotationElement";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _position
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- if (!target.hasPosition()) { return null; }
- return new java.lang.Integer(target.getPosition());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setPosition( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _position
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _colour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- if (!target.hasColour()) { return null; }
- return new java.lang.Integer(target.getColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColour();
- return;
- }
- target.setColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _displayCharacter
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getDisplayCharacter();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setDisplayCharacter( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _displayCharacter
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class AnnotationElementDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationElementDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "annotationElement";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _position
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_position", "position",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ if (!target.hasPosition())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setDescription( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getPosition());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setPosition(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _secondaryStructure
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getSecondaryStructure();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setSecondaryStructure( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _secondaryStructure
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- typeValidator.setLength(1);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _position
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_colour", "colour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ if (!target.hasColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- if (!target.hasValue()) { return null; }
- return new java.lang.Float(target.getValue());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteValue();
- return;
- }
- target.setValue( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ return new java.lang.Integer(target.getColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColour();
+ return;
+ }
+ target.setColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+ // -- _displayCharacter
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_displayCharacter",
+ "displayCharacter", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ return target.getDisplayCharacter();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ target.setDisplayCharacter((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _displayCharacter
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_description", "description",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ return target.getDescription();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AnnotationElement.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ target.setDescription((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _secondaryStructure
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_secondaryStructure",
+ "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ return target.getSecondaryStructure();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ target.setSecondaryStructure((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _secondaryStructure
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ typeValidator.setLength(1);
}
+ desc.setValidator(fieldValidator);
+ // -- _value
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_value", "value",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ if (!target.hasValue())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getValue());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteValue();
+ return;
+ }
+ target.setValue(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _value
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationElement.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.CalcIdParam;
*
* @version $Revision$ $Date$
*/
-public class CalcIdParamDescriptor extends jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public CalcIdParamDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "calcIdParam";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _calcId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_calcId", "calcId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- CalcIdParam target = (CalcIdParam) object;
- return target.getCalcId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- CalcIdParam target = (CalcIdParam) object;
- target.setCalcId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _calcId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class CalcIdParamDescriptor
+ extends
+ jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public CalcIdParamDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "calcIdParam";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _calcId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_calcId", "calcId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ return target.getCalcId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ target.setCalcId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _needsUpdate
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- CalcIdParam target = (CalcIdParam) object;
- if (!target.hasNeedsUpdate()) { return null; }
- return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- CalcIdParam target = (CalcIdParam) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteNeedsUpdate();
- return;
- }
- target.setNeedsUpdate( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _needsUpdate
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _calcId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _needsUpdate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ if (!target.hasNeedsUpdate())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _autoUpdate
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- CalcIdParam target = (CalcIdParam) object;
- if (!target.hasAutoUpdate()) { return null; }
- return (target.getAutoUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- CalcIdParam target = (CalcIdParam) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setAutoUpdate( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _autoUpdate
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteNeedsUpdate();
+ return;
+ }
+ target.setNeedsUpdate(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _needsUpdate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _autoUpdate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ if (!target.hasAutoUpdate())
+ {
+ return null;
+ }
+ return (target.getAutoUpdate() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setAutoUpdate(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _autoUpdate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.CalcIdParam.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.CalcIdParam.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Colour;
*
* @version $Revision$ $Date$
*/
-public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ColourDescriptor() {
- super();
- _xmlName = "colour";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _RGB
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- return target.getRGB();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- target.setRGB( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _RGB
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class ColourDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public ColourDescriptor()
+ {
+ super();
+ _xmlName = "colour";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "Name",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ return target.getName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _minRGB
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- return target.getMinRGB();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- target.setMinRGB( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _minRGB
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _RGB
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_RGB", "RGB",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ return target.getRGB();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ target.setRGB((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _threshType
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- return target.getThreshType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- target.setThreshType( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshType
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _RGB
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _minRGB
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_minRGB", "minRGB",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ return target.getMinRGB();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ target.setMinRGB((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- if (!target.hasThreshold()) { return null; }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshold();
- return;
- }
- target.setThreshold( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _minRGB
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshType
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_threshType", "threshType",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ return target.getThreshType();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ target.setThreshType((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _max
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- if (!target.hasMax()) { return null; }
- return new java.lang.Float(target.getMax());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMax();
- return;
- }
- target.setMax( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _max
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _threshType
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ if (!target.hasThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _min
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- if (!target.hasMin()) { return null; }
- return new java.lang.Float(target.getMin());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMin();
- return;
- }
- target.setMin( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _min
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ return new java.lang.Float(target.getThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colourByLabel
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- if (!target.hasColourByLabel()) { return null; }
- return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColourByLabel();
- return;
- }
- target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourByLabel
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _max
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_max", "max",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ if (!target.hasMax())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _autoScale
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Colour target = (Colour) object;
- if (!target.hasAutoScale()) { return null; }
- return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Colour target = (Colour) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAutoScale();
- return;
- }
- target.setAutoScale( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _autoScale
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Float(target.getMax());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMax();
+ return;
+ }
+ target.setMax(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+ // -- validation code for: _max
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _min
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_min", "min",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ if (!target.hasMin())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getMin());
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMin();
+ return;
+ }
+ target.setMin(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _min
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ // -- _colourByLabel
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ if (!target.hasColourByLabel())
+ {
+ return null;
+ }
+ return (target.getColourByLabel() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Colour.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColourByLabel();
+ return;
+ }
+ target.setColourByLabel(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _colourByLabel
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _autoScale
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_autoScale", "autoScale",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Colour target = (Colour) object;
+ if (!target.hasAutoScale())
+ {
+ return null;
+ }
+ return (target.getAutoScale() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Colour target = (Colour) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAutoScale();
+ return;
+ }
+ target.setAutoScale(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _autoScale
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Colour.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.DBRef;
*
* @version $Revision$ $Date$
*/
-public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DBRefDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "DBRef";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _source
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DBRef target = (DBRef) object;
- return target.getSource();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DBRef target = (DBRef) object;
- target.setSource( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _source
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DBRef target = (DBRef) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DBRef target = (DBRef) object;
- target.setVersion( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _accessionId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DBRef target = (DBRef) object;
- return target.getAccessionId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DBRef target = (DBRef) object;
- target.setAccessionId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _accessionId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _mapping
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DBRef target = (DBRef) object;
- return target.getMapping();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DBRef target = (DBRef) object;
- target.setMapping( (jalview.schemabinding.version2.Mapping) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Mapping();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapping
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- }
+public class DBRefDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
- //-----------/
- //- Methods -/
- //-----------/
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public DBRefDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "DBRef";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _source
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_source", "source",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DBRef target = (DBRef) object;
+ return target.getSource();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DBRef target = (DBRef) object;
+ target.setSource((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _source
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _version
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_version", "version",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DBRef target = (DBRef) object;
+ return target.getVersion();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.DBRef.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DBRef target = (DBRef) object;
+ target.setVersion((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _version
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _accessionId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_accessionId", "accessionId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DBRef target = (DBRef) object;
+ return target.getAccessionId();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DBRef target = (DBRef) object;
+ target.setAccessionId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _accessionId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _mapping
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Mapping.class, "_mapping",
+ "Mapping", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DBRef target = (DBRef) object;
+ return target.getMapping();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DBRef target = (DBRef) object;
+ target.setMapping((jalview.schemabinding.version2.Mapping) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Mapping();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _mapping
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.DBRef.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Feature;
*
* @version $Revision$ $Date$
*/
-public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public FeatureDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "feature";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _begin
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- if (!target.hasBegin()) { return null; }
- return new java.lang.Integer(target.getBegin());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setBegin( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _begin
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _type
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- target.setType( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _type
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- target.setDescription( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _status
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- return target.getStatus();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- target.setStatus( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _status
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _featureGroup
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- return target.getFeatureGroup();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- target.setFeatureGroup( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _featureGroup
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _score
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- if (!target.hasScore()) { return null; }
- return new java.lang.Float(target.getScore());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteScore();
- return;
- }
- target.setScore( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _score
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+public class FeatureDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public FeatureDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "feature";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _begin
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_begin", "begin",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ if (!target.hasBegin())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _otherDataList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Feature target = (Feature) object;
- return target.getOtherData();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Feature target = (Feature) object;
- target.addOtherData( (jalview.schemabinding.version2.OtherData) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Feature target = (Feature) object;
- target.removeAllOtherData();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.OtherData();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _otherDataList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ return new java.lang.Integer(target.getBegin());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setBegin(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _begin
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ if (!target.hasEnd())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getEnd());
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _type
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_type", "type",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ return target.getType();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.setType((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Feature.class;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _type
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_description", "description",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ return target.getDescription();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.setDescription((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _status
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_status", "status",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ return target.getStatus();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.setStatus((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _status
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _featureGroup
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_featureGroup", "featureGroup",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ return target.getFeatureGroup();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.setFeatureGroup((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _featureGroup
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _score
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_score", "score",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ if (!target.hasScore())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getScore());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScore();
+ return;
+ }
+ target.setScore(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _score
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- _otherDataList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.OtherData.class,
+ "_otherDataList", "otherData",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Feature target = (Feature) object;
+ return target.getOtherData();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.addOtherData((jalview.schemabinding.version2.OtherData) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Feature target = (Feature) object;
+ target.removeAllOtherData();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.OtherData();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _otherDataList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Feature.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.FeatureSettings;
*
* @version $Revision$ $Date$
*/
-public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public FeatureSettingsDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "FeatureSettings";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _settingList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- FeatureSettings target = (FeatureSettings) object;
- return target.getSetting();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- FeatureSettings target = (FeatureSettings) object;
- target.addSetting( (jalview.schemabinding.version2.Setting) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- FeatureSettings target = (FeatureSettings) object;
- target.removeAllSetting();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Setting();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _settingList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class FeatureSettingsDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public FeatureSettingsDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "FeatureSettings";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _settingList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Setting.class, "_settingList",
+ "setting", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ return target.getSetting();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ target.addSetting((jalview.schemabinding.version2.Setting) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _groupList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- FeatureSettings target = (FeatureSettings) object;
- return target.getGroup();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- FeatureSettings target = (FeatureSettings) object;
- target.addGroup( (jalview.schemabinding.version2.Group) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- FeatureSettings target = (FeatureSettings) object;
- target.removeAllGroup();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Group();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _groupList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ target.removeAllSetting();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Setting();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _settingList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _groupList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Group.class, "_groupList",
+ "group", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ return target.getGroup();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ target.addGroup((jalview.schemabinding.version2.Group) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ FeatureSettings target = (FeatureSettings) object;
+ target.removeAllGroup();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Group();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _groupList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.FeatureSettings.class;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.FeatureSettings.class;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import jalview.schemabinding.version2.Features;
/**
* Class FeaturesDescriptor.
*
* @version $Revision$ $Date$
*/
-public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public FeaturesDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "features";
- _elementDefinition = true;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Features.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+public class FeaturesDescriptor extends
+ jalview.schemabinding.version2.descriptors.FeatureDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public FeaturesDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "features";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Features.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Group;
*
* @version $Revision$ $Date$
*/
-public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public GroupDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "group";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Group target = (Group) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Group target = (Group) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _display
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Group target = (Group) object;
- if (!target.hasDisplay()) { return null; }
- return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Group target = (Group) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setDisplay( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _display
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+public class GroupDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public GroupDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "group";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "name",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Group target = (Group) object;
+ return target.getName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Group target = (Group) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _display
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_display", "display",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Group target = (Group) object;
+ if (!target.hasDisplay())
+ {
+ return null;
+ }
+ return (target.getDisplay() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Group target = (Group) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setDisplay(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _display
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Group.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Group.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.HiddenColumns;
*
* @version $Revision$ $Date$
*/
-public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public HiddenColumnsDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "hiddenColumns";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- HiddenColumns target = (HiddenColumns) object;
- if (!target.hasStart()) { return null; }
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- HiddenColumns target = (HiddenColumns) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteStart();
- return;
- }
- target.setStart( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class HiddenColumnsDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public HiddenColumnsDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "hiddenColumns";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _start
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_start", "start",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ HiddenColumns target = (HiddenColumns) object;
+ if (!target.hasStart())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- HiddenColumns target = (HiddenColumns) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- HiddenColumns target = (HiddenColumns) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteEnd();
- return;
- }
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getStart());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ HiddenColumns target = (HiddenColumns) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteStart();
+ return;
+ }
+ target.setStart(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _start
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ HiddenColumns target = (HiddenColumns) object;
+ if (!target.hasEnd())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getEnd());
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ HiddenColumns target = (HiddenColumns) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteEnd();
+ return;
+ }
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.HiddenColumns.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.HiddenColumns.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.JGroup;
*
* @version $Revision$ $Date$
*/
-public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JGroupDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "JGroup";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasStart()) { return null; }
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteStart();
- return;
- }
- target.setStart( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class JGroupDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroupDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "JGroup";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _start
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_start", "start",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasStart())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteEnd();
- return;
- }
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getStart());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteStart();
+ return;
+ }
+ target.setStart(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _start
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasEnd())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _colour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- return target.getColour();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- target.setColour( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getEnd());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteEnd();
+ return;
+ }
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _consThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasConsThreshold()) { return null; }
- return new java.lang.Integer(target.getConsThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteConsThreshold();
- return;
- }
- target.setConsThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _consThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "name",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _pidThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasPidThreshold()) { return null; }
- return new java.lang.Integer(target.getPidThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePidThreshold();
- return;
- }
- target.setPidThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pidThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_colour", "colour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getColour();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setColour((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _outlineColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasOutlineColour()) { return null; }
- return new java.lang.Integer(target.getOutlineColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteOutlineColour();
- return;
- }
- target.setOutlineColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _outlineColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _consThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasConsThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _displayBoxes
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasDisplayBoxes()) { return null; }
- return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteDisplayBoxes();
- return;
- }
- target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _displayBoxes
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getConsThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteConsThreshold();
+ return;
+ }
+ target.setConsThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _displayText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasDisplayText()) { return null; }
- return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteDisplayText();
- return;
- }
- target.setDisplayText( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _displayText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _consThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pidThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasPidThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _colourText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasColourText()) { return null; }
- return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColourText();
- return;
- }
- target.setColourText( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getPidThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePidThreshold();
+ return;
+ }
+ target.setPidThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _textCol1
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasTextCol1()) { return null; }
- return new java.lang.Integer(target.getTextCol1());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextCol1();
- return;
- }
- target.setTextCol1( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textCol1
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pidThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _outlineColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_outlineColour", "outlineColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasOutlineColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getOutlineColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteOutlineColour();
+ return;
+ }
+ target.setOutlineColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _textCol2
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasTextCol2()) { return null; }
- return new java.lang.Integer(target.getTextCol2());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextCol2();
- return;
- }
- target.setTextCol2( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textCol2
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _outlineColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _displayBoxes
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasDisplayBoxes())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _textColThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasTextColThreshold()) { return null; }
- return new java.lang.Integer(target.getTextColThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextColThreshold();
- return;
- }
- target.setTextColThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textColThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteDisplayBoxes();
+ return;
+ }
+ target.setDisplayBoxes(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _showUnconserved
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasShowUnconserved()) { return null; }
- return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowUnconserved();
- return;
- }
- target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showUnconserved
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _displayBoxes
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _displayText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_displayText", "displayText",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasDisplayText())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _ignoreGapsinConsensus
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasIgnoreGapsinConsensus()) { return null; }
- return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteIgnoreGapsinConsensus();
- return;
- }
- target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ignoreGapsinConsensus
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getDisplayText() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteDisplayText();
+ return;
+ }
+ target.setDisplayText(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _showConsensusHistogram
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasShowConsensusHistogram()) { return null; }
- return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowConsensusHistogram();
- return;
- }
- target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showConsensusHistogram
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _displayText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_colourText", "colourText",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasColourText())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _showSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasShowSequenceLogo()) { return null; }
- return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowSequenceLogo();
- return;
- }
- target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getColourText() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColourText();
+ return;
+ }
+ target.setColourText(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _normaliseSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_normaliseSequenceLogo", "normaliseSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- if (!target.hasNormaliseSequenceLogo()) { return null; }
- return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteNormaliseSequenceLogo();
- return;
- }
- target.setNormaliseSequenceLogo( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _normaliseSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colourText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _textCol1
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textCol1", "textCol1",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasTextCol1())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getTextCol1());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextCol1();
+ return;
+ }
+ target.setTextCol1(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _seqList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- return target.getSeq();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- target.addSeq( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JGroup target = (JGroup) object;
- target.removeAllSeq();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _seqList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _textCol1
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _textCol2
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textCol2", "textCol2",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasTextCol2())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _annotationColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "annotationColours", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JGroup target = (JGroup) object;
- return target.getAnnotationColours();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JGroup target = (JGroup) object;
- target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.AnnotationColours();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
+ return new java.lang.Integer(target.getTextCol2());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextCol2();
+ return;
+ }
+ target.setTextCol2(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _textCol2
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _textColThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textColThreshold",
+ "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasTextColThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getTextColThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextColThreshold();
+ return;
+ }
+ target.setTextColThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _textColThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showUnconserved
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasShowUnconserved())
+ {
+ return null;
+ }
+ return (target.getShowUnconserved() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowUnconserved();
+ return;
+ }
+ target.setShowUnconserved(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showUnconserved
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _ignoreGapsinConsensus
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",
+ "ignoreGapsinConsensus",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasIgnoreGapsinConsensus())
+ {
+ return null;
+ }
+ return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIgnoreGapsinConsensus();
+ return;
+ }
+ target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _ignoreGapsinConsensus
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _showConsensusHistogram
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showConsensusHistogram",
+ "showConsensusHistogram",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasShowConsensusHistogram())
+ {
+ return null;
+ }
+ return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.JGroup.class;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowConsensusHistogram();
+ return;
+ }
+ target.setShowConsensusHistogram(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showConsensusHistogram
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _showSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showSequenceLogo",
+ "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasShowSequenceLogo())
+ {
+ return null;
+ }
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowSequenceLogo();
+ return;
+ }
+ target.setShowSequenceLogo(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _normaliseSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_normaliseSequenceLogo",
+ "normaliseSequenceLogo",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ if (!target.hasNormaliseSequenceLogo())
+ {
+ return null;
+ }
+ return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteNormaliseSequenceLogo();
+ return;
+ }
+ target.setNormaliseSequenceLogo(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _normaliseSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getId();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _seqList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_seqList", "seq",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getSeq();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.addSeq((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.removeAllSeq();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _seqList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _annotationColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ "_annotationColours", "annotationColours",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getAnnotationColours();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AnnotationColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _annotationColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.JGroup.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.JSeq;
*
* @version $Revision$ $Date$
*/
-public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JSeqDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "JSeq";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _colour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- if (!target.hasColour()) { return null; }
- return new java.lang.Integer(target.getColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColour();
- return;
- }
- target.setColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class JSeqDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JSeqDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "JSeq";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _colour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_colour", "colour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ if (!target.hasColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- if (!target.hasStart()) { return null; }
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setStart( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColour();
+ return;
+ }
+ target.setColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _start
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_start", "start",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ if (!target.hasStart())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return new java.lang.Integer(target.getStart());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setStart(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _hidden
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- if (!target.hasHidden()) { return null; }
- return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteHidden();
- return;
- }
- target.setHidden( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _hidden
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _start
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ if (!target.hasEnd())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _featuresList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- return target.getFeatures();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- target.addFeatures( (jalview.schemabinding.version2.Features) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JSeq target = (JSeq) object;
- target.removeAllFeatures();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Features();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _featuresList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ return new java.lang.Integer(target.getEnd());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _pdbidsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- return target.getPdbids();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JSeq target = (JSeq) object;
- target.removeAllPdbids();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Pdbids();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pdbidsList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _hiddenSequencesList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- return target.getHiddenSequences();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.addHiddenSequences( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JSeq target = (JSeq) object;
- target.removeAllHiddenSequences();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _hiddenSequencesList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _hidden
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_hidden", "hidden",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ if (!target.hasHidden())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _rnaViewerList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.RnaViewer.class, "_rnaViewerList", "rnaViewer", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JSeq target = (JSeq) object;
- return target.getRnaViewer();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JSeq target = (JSeq) object;
- target.addRnaViewer( (jalview.schemabinding.version2.RnaViewer) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JSeq target = (JSeq) object;
- target.removeAllRnaViewer();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.RnaViewer();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _rnaViewerList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ return (target.getHidden() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHidden();
+ return;
+ }
+ target.setHidden(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _hidden
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+ // -- _featuresList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Features.class, "_featuresList",
+ "features", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getFeatures();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.addFeatures((jalview.schemabinding.version2.Features) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.removeAllFeatures();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Features();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.JSeq.class;
+ // -- validation code for: _featuresList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _pdbidsList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
+ "pdbids", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getPdbids();
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.removeAllPdbids();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Pdbids();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pdbidsList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _hiddenSequencesList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_hiddenSequencesList",
+ "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getHiddenSequences();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.addHiddenSequences(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.removeAllHiddenSequences();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _hiddenSequencesList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _rnaViewerList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.RnaViewer.class,
+ "_rnaViewerList", "rnaViewer",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getRnaViewer();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ target.removeAllRnaViewer();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.RnaViewer();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rnaViewerList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.JSeq.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.JalviewModel;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModelDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "JalviewModel";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _creationDate
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModel target = (JalviewModel) object;
- return target.getCreationDate();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModel target = (JalviewModel) object;
- target.setCreationDate( (java.util.Date) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new java.util.Date();
- }
- };
- handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
- desc.setImmutable(true);
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _creationDate
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModel target = (JalviewModel) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModel target = (JalviewModel) object;
- target.setVersion( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _vamsasModel
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModel target = (JalviewModel) object;
- return target.getVamsasModel();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModel target = (JalviewModel) object;
- target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.VamsasModel();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _vamsasModel
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _jalviewModelSequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModel target = (JalviewModel) object;
- return target.getJalviewModelSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModel target = (JalviewModel) object;
- target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.JalviewModelSequence();
- }
- };
- desc.setHandler(handler);
- desc.setContainer(true);
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _jalviewModelSequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
+public class JalviewModelDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModelDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "JalviewModel";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _creationDate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.util.Date.class, "_creationDate", "creationDate",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModel target = (JalviewModel) object;
+ return target.getCreationDate();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModel target = (JalviewModel) object;
+ target.setCreationDate((java.util.Date) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new java.util.Date();
+ }
+ };
+ handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
+ desc.setImmutable(true);
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _creationDate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _version
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_version", "version",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModel target = (JalviewModel) object;
+ return target.getVersion();
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModel target = (JalviewModel) object;
+ target.setVersion((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _version
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _vamsasModel
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.VamsasModel.class,
+ "_vamsasModel", "vamsasModel",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModel target = (JalviewModel) object;
+ return target.getVamsasModel();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.JalviewModel.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModel target = (JalviewModel) object;
+ target.setVamsasModel((jalview.schemabinding.version2.VamsasModel) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.VamsasModel();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _vamsasModel
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _jalviewModelSequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.JalviewModelSequence.class,
+ "_jalviewModelSequence", "-error-if-this-is-used-",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModel target = (JalviewModel) object;
+ return target.getJalviewModelSequence();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModel target = (JalviewModel) object;
+ target.setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.JalviewModelSequence();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setContainer(true);
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _jalviewModelSequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.JalviewModel.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.JalviewModelSequence;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewModelSequenceDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _JSeqList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getJSeq();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.addJSeq( (jalview.schemabinding.version2.JSeq) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.removeAllJSeq();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.JSeq();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _JSeqList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class JalviewModelSequenceDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModelSequenceDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _JSeqList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getJSeq();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addJSeq((jalview.schemabinding.version2.JSeq) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _JGroupList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getJGroup();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.addJGroup( (jalview.schemabinding.version2.JGroup) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.removeAllJGroup();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.JGroup();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _JGroupList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllJSeq();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _viewportList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getViewport();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.addViewport( (jalview.schemabinding.version2.Viewport) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.removeAllViewport();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Viewport();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _viewportList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.JSeq();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _JSeqList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _JGroupList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.JGroup.class, "_JGroupList",
+ "JGroup", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getJGroup();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addJGroup((jalview.schemabinding.version2.JGroup) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _userColoursList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getUserColours();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.addUserColours( (jalview.schemabinding.version2.UserColours) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.removeAllUserColours();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.UserColours();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _userColoursList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllJGroup();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getTree();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.addTree( (jalview.schemabinding.version2.Tree) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.removeAllTree();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Tree();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _treeList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.JGroup();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _JGroupList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _viewportList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Viewport.class, "_viewportList",
+ "Viewport", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getViewport();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addViewport((jalview.schemabinding.version2.Viewport) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _featureSettings
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewModelSequence target = (JalviewModelSequence) object;
- return target.getFeatureSettings();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewModelSequence target = (JalviewModelSequence) object;
- target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.FeatureSettings();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _featureSettings
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllViewport();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Viewport();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _viewportList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _userColoursList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.UserColours.class,
+ "_userColoursList", "UserColours",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getUserColours();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addUserColours((jalview.schemabinding.version2.UserColours) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllUserColours();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.UserColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _userColoursList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _treeList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Tree.class, "_treeList", "tree",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getTree();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.JalviewModelSequence.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addTree((jalview.schemabinding.version2.Tree) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllTree();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Tree();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ // -- validation code for: _treeList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _featureSettings
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.FeatureSettings.class,
+ "_featureSettings", "FeatureSettings",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getFeatureSettings();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.FeatureSettings();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _featureSettings
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.JalviewModelSequence.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Colour;
*
* @version $Revision$ $Date$
*/
-public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewUserColoursDescriptor() {
- super();
- _nsURI = "www.jalview.org/colours";
- _xmlName = "JalviewUserColours";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _schemeName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewUserColours target = (JalviewUserColours) object;
- return target.getSchemeName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewUserColours target = (JalviewUserColours) object;
- target.setSchemeName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _schemeName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewUserColours target = (JalviewUserColours) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewUserColours target = (JalviewUserColours) object;
- target.setVersion( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _colourList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- JalviewUserColours target = (JalviewUserColours) object;
- return target.getColour();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- JalviewUserColours target = (JalviewUserColours) object;
- target.addColour( (Colour) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- JalviewUserColours target = (JalviewUserColours) object;
- target.removeAllColour();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new Colour();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class JalviewUserColoursDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewUserColoursDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org/colours";
+ _xmlName = "JalviewUserColours";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _schemeName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_schemeName", "schemeName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ return target.getSchemeName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ target.setSchemeName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _schemeName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+ // -- _version
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_version", "Version",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ return target.getVersion();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ target.setVersion((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _version
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _colourList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ Colour.class, "_colourList", "colour",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ return target.getColour();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.JalviewUserColours.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ target.addColour((Colour) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ JalviewUserColours target = (JalviewUserColours) object;
+ target.removeAllColour();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new Colour();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ // -- validation code for: _colourList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.JalviewUserColours.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.MapListFrom;
*
* @version $Revision$ $Date$
*/
-public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListFromDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "mapListFrom";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListFrom target = (MapListFrom) object;
- if (!target.hasStart()) { return null; }
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListFrom target = (MapListFrom) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setStart( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class MapListFromDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListFromDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "mapListFrom";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _start
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_start", "start",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListFrom target = (MapListFrom) object;
+ if (!target.hasStart())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListFrom target = (MapListFrom) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListFrom target = (MapListFrom) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getStart());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListFrom target = (MapListFrom) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setStart(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _start
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListFrom target = (MapListFrom) object;
+ if (!target.hasEnd())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getEnd());
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListFrom target = (MapListFrom) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.MapListFrom.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.MapListFrom.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.MapListTo;
*
* @version $Revision$ $Date$
*/
-public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListToDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "mapListTo";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListTo target = (MapListTo) object;
- if (!target.hasStart()) { return null; }
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListTo target = (MapListTo) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setStart( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class MapListToDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListToDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "mapListTo";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _start
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_start", "start",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListTo target = (MapListTo) object;
+ if (!target.hasStart())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListTo target = (MapListTo) object;
- if (!target.hasEnd()) { return null; }
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListTo target = (MapListTo) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setEnd( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getStart());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListTo target = (MapListTo) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setStart(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _start
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _end
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_end", "end",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListTo target = (MapListTo) object;
+ if (!target.hasEnd())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getEnd());
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListTo target = (MapListTo) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setEnd(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _end
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.MapListTo.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.MapListTo.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.MapListType;
*
* @version $Revision$ $Date$
*/
-public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MapListTypeDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "mapListType";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _mapFromUnit
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListType target = (MapListType) object;
- if (!target.hasMapFromUnit()) { return null; }
- return new java.lang.Long(target.getMapFromUnit());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListType target = (MapListType) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setMapFromUnit( ((java.lang.Long) value).longValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapFromUnit
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.LongValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(1L);
- }
- desc.setValidator(fieldValidator);
- //-- _mapToUnit
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListType target = (MapListType) object;
- if (!target.hasMapToUnit()) { return null; }
- return new java.lang.Long(target.getMapToUnit());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListType target = (MapListType) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setMapToUnit( ((java.lang.Long) value).longValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapToUnit
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.LongValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(1L);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _mapListFromList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListType target = (MapListType) object;
- return target.getMapListFrom();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListType target = (MapListType) object;
- target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- MapListType target = (MapListType) object;
- target.removeAllMapListFrom();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.MapListFrom();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapListFromList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class MapListTypeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MapListTypeDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "mapListType";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _mapFromUnit
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListType target = (MapListType) object;
+ if (!target.hasMapFromUnit())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _mapListToList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MapListType target = (MapListType) object;
- return target.getMapListTo();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MapListType target = (MapListType) object;
- target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- MapListType target = (MapListType) object;
- target.removeAllMapListTo();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.MapListTo();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapListToList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ return new java.lang.Long(target.getMapFromUnit());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setMapFromUnit(((java.lang.Long) value).longValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _mapFromUnit
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.LongValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(1L);
}
+ desc.setValidator(fieldValidator);
+ // -- _mapToUnit
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Long.TYPE, "_mapToUnit", "mapToUnit",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListType target = (MapListType) object;
+ if (!target.hasMapToUnit())
+ {
+ return null;
+ }
+ return new java.lang.Long(target.getMapToUnit());
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ target.setMapToUnit(((java.lang.Long) value).longValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _mapToUnit
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.LongValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(1L);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.MapListType.class;
- }
+ // -- _mapListFromList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.MapListFrom.class,
+ "_mapListFromList", "mapListFrom",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListType target = (MapListType) object;
+ return target.getMapListFrom();
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ target.addMapListFrom((jalview.schemabinding.version2.MapListFrom) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ target.removeAllMapListFrom();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.MapListFrom();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _mapListFromList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _mapListToList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.MapListTo.class,
+ "_mapListToList", "mapListTo",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MapListType target = (MapListType) object;
+ return target.getMapListTo();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ target.addMapListTo((jalview.schemabinding.version2.MapListTo) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ MapListType target = (MapListType) object;
+ target.removeAllMapListTo();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.MapListTo();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _mapListToList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.MapListType.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.MappingChoice;
*
* @version $Revision$ $Date$
*/
-public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MappingChoiceDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsChoice();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _sequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MappingChoice target = (MappingChoice) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MappingChoice target = (MappingChoice) object;
- target.setSequence( (jalview.schemabinding.version2.Sequence) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Sequence();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _dseqFor
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- MappingChoice target = (MappingChoice) object;
- return target.getDseqFor();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- MappingChoice target = (MappingChoice) object;
- target.setDseqFor( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dseqFor
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class MappingChoiceDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MappingChoiceDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsChoice();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _sequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Sequence.class, "_sequence",
+ "Sequence", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MappingChoice target = (MappingChoice) object;
+ return target.getSequence();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MappingChoice target = (MappingChoice) object;
+ target.setSequence((jalview.schemabinding.version2.Sequence) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Sequence();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _dseqFor
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_dseqFor", "dseqFor",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ MappingChoice target = (MappingChoice) object;
+ return target.getDseqFor();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ MappingChoice target = (MappingChoice) object;
+ target.setDseqFor((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _dseqFor
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.MappingChoice.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.MappingChoice.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Mapping;
*
* @version $Revision$ $Date$
*/
-public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public MappingDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "Mapping";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsChoice();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _mappingChoice
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Mapping target = (Mapping) object;
- return target.getMappingChoice();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Mapping target = (Mapping) object;
- target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.MappingChoice();
- }
- };
- desc.setHandler(handler);
- desc.setContainer(true);
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mappingChoice
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
+public class MappingDescriptor extends
+ jalview.schemabinding.version2.descriptors.MapListTypeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public MappingDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "Mapping";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsChoice();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _mappingChoice
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.MappingChoice.class,
+ "_mappingChoice", "-error-if-this-is-used-",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Mapping target = (Mapping) object;
+ return target.getMappingChoice();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Mapping target = (Mapping) object;
+ target.setMappingChoice((jalview.schemabinding.version2.MappingChoice) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Mapping.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.MappingChoice();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setContainer(true);
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _mappingChoice
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Mapping.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.OtherData;
*
* @version $Revision$ $Date$
*/
-public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public OtherDataDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "otherData";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _key
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- OtherData target = (OtherData) object;
- return target.getKey();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- OtherData target = (OtherData) object;
- target.setKey( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _key
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- OtherData target = (OtherData) object;
- return target.getValue();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- OtherData target = (OtherData) object;
- target.setValue( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class OtherDataDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public OtherDataDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "otherData";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _key
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_key", "key",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ OtherData target = (OtherData) object;
+ return target.getKey();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ OtherData target = (OtherData) object;
+ target.setKey((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _key
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _value
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_value", "value",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ OtherData target = (OtherData) object;
+ return target.getValue();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ OtherData target = (OtherData) object;
+ target.setValue((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.OtherData.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _value
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.OtherData.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Pdbentry;
*
* @version $Revision$ $Date$
*/
-public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PdbentryDescriptor() {
- super();
- _xmlName = "pdbentry";
- _elementDefinition = false;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Pdbentry target = (Pdbentry) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Pdbentry target = (Pdbentry) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _type
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Pdbentry target = (Pdbentry) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Pdbentry target = (Pdbentry) object;
- target.setType( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _type
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _file
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Pdbentry target = (Pdbentry) object;
- return target.getFile();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Pdbentry target = (Pdbentry) object;
- target.setFile( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _file
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _items
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Pdbentry target = (Pdbentry) object;
- return target.getPdbentryItem();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Pdbentry target = (Pdbentry) object;
- target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Pdbentry target = (Pdbentry) object;
- target.removeAllPdbentryItem();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.PdbentryItem();
- }
- };
- desc.setHandler(handler);
- desc.setContainer(true);
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _items
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- }
+public class PdbentryDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
- //-----------/
- //- Methods -/
- //-----------/
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public PdbentryDescriptor()
+ {
+ super();
+ _xmlName = "pdbentry";
+ _elementDefinition = false;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Pdbentry target = (Pdbentry) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Pdbentry target = (Pdbentry) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _type
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_type", "type",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Pdbentry target = (Pdbentry) object;
+ return target.getType();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Pdbentry.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Pdbentry target = (Pdbentry) object;
+ target.setType((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _type
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _file
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_file", "file",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Pdbentry target = (Pdbentry) object;
+ return target.getFile();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Pdbentry target = (Pdbentry) object;
+ target.setFile((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _file
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _items
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PdbentryItem.class, "_items",
+ (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Pdbentry target = (Pdbentry) object;
+ return target.getPdbentryItem();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Pdbentry target = (Pdbentry) object;
+ target.addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Pdbentry target = (Pdbentry) object;
+ target.removeAllPdbentryItem();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PdbentryItem();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setContainer(true);
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ // -- validation code for: _items
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Pdbentry.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.PdbentryItem;
*
* @version $Revision$ $Date$
*/
-public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PdbentryItemDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "pdbentry";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- PdbentryItem target = (PdbentryItem) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- PdbentryItem target = (PdbentryItem) object;
- target.addProperty( (jalview.schemabinding.version2.Property) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- PdbentryItem target = (PdbentryItem) object;
- target.removeAllProperty();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class PdbentryItemDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PdbentryItemDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "pdbentry";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Property.class, "_propertyList",
+ "property", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PdbentryItem target = (PdbentryItem) object;
+ return target.getProperty();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PdbentryItem target = (PdbentryItem) object;
+ target.addProperty((jalview.schemabinding.version2.Property) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.PdbentryItem.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ PdbentryItem target = (PdbentryItem) object;
+ target.removeAllProperty();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PdbentryItem.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Pdbids;
*
* @version $Revision$ $Date$
*/
-public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PdbidsDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "pdbids";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _structureStateList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Pdbids target = (Pdbids) object;
- return target.getStructureState();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Pdbids target = (Pdbids) object;
- target.addStructureState( (jalview.schemabinding.version2.StructureState) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Pdbids target = (Pdbids) object;
- target.removeAllStructureState();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.StructureState();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _structureStateList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+public class PdbidsDescriptor extends
+ jalview.schemabinding.version2.descriptors.PdbentryDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PdbidsDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "pdbids";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _structureStateList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.StructureState.class,
+ "_structureStateList", "structureState",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Pdbids target = (Pdbids) object;
+ return target.getStructureState();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Pdbids target = (Pdbids) object;
+ target.addStructureState((jalview.schemabinding.version2.StructureState) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Pdbids.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Pdbids target = (Pdbids) object;
+ target.removeAllStructureState();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.StructureState();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _structureStateList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Pdbids.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Property;
*
* @version $Revision$ $Date$
*/
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public PropertyDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "property";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Property target = (Property) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Property target = (Property) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Property target = (Property) object;
- return target.getValue();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Property target = (Property) object;
- target.setValue( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class PropertyDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PropertyDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "property";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "name",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Property target = (Property) object;
+ return target.getName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Property target = (Property) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _value
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_value", "value",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Property target = (Property) object;
+ return target.getValue();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Property target = (Property) object;
+ target.setValue((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Property.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _value
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Property.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.RnaViewer;
*
* @version $Revision$ $Date$
*/
-public class RnaViewerDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public RnaViewerDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "rnaViewer";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- target.setTitle( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _viewId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- return target.getViewId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- target.setViewId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _viewId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class RnaViewerDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public RnaViewerDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "rnaViewer";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getTitle();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _dividerLocation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasDividerLocation()) { return null; }
- return new java.lang.Integer(target.getDividerLocation());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteDividerLocation();
- return;
- }
- target.setDividerLocation( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dividerLocation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _viewId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_viewId", "viewId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getViewId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ target.setViewId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _selectedRna
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_selectedRna", "selectedRna", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasSelectedRna()) { return null; }
- return new java.lang.Integer(target.getSelectedRna());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteSelectedRna();
- return;
- }
- target.setSelectedRna( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _selectedRna
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _viewId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _dividerLocation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasDividerLocation())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _width
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasWidth()) { return null; }
- return new java.lang.Integer(target.getWidth());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteWidth();
- return;
- }
- target.setWidth( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _width
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getDividerLocation());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteDividerLocation();
+ return;
+ }
+ target.setDividerLocation(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _height
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasHeight()) { return null; }
- return new java.lang.Integer(target.getHeight());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteHeight();
- return;
- }
- target.setHeight( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _height
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _dividerLocation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _selectedRna
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_selectedRna", "selectedRna",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasSelectedRna())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _xpos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasXpos()) { return null; }
- return new java.lang.Integer(target.getXpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteXpos();
- return;
- }
- target.setXpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _xpos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Integer(target.getSelectedRna());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteSelectedRna();
+ return;
+ }
+ target.setSelectedRna(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _ypos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- if (!target.hasYpos()) { return null; }
- return new java.lang.Integer(target.getYpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteYpos();
- return;
- }
- target.setYpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ypos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _selectedRna
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasWidth())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _secondaryStructureList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SecondaryStructure.class, "_secondaryStructureList", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- RnaViewer target = (RnaViewer) object;
- return target.getSecondaryStructure();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- RnaViewer target = (RnaViewer) object;
- target.addSecondaryStructure( (jalview.schemabinding.version2.SecondaryStructure) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- RnaViewer target = (RnaViewer) object;
- target.removeAllSecondaryStructure();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.SecondaryStructure();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _secondaryStructureList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
+ return new java.lang.Integer(target.getWidth());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.RnaViewer.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _secondaryStructureList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SecondaryStructure.class,
+ "_secondaryStructureList", "secondaryStructure",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getSecondaryStructure();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ target.addSecondaryStructure((jalview.schemabinding.version2.SecondaryStructure) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ RnaViewer target = (RnaViewer) object;
+ target.removeAllSecondaryStructure();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SecondaryStructure();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _secondaryStructureList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.RnaViewer.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.SecondaryStructure;
*
* @version $Revision$ $Date$
*/
-public class SecondaryStructureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SecondaryStructureDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "secondaryStructure";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SecondaryStructure target = (SecondaryStructure) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SecondaryStructure target = (SecondaryStructure) object;
- target.setTitle( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class SecondaryStructureDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SecondaryStructureDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "secondaryStructure";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getTitle();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _annotationId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotationId", "annotationId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SecondaryStructure target = (SecondaryStructure) object;
- return target.getAnnotationId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SecondaryStructure target = (SecondaryStructure) object;
- target.setAnnotationId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _annotationId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_annotationId", "annotationId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getAnnotationId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setAnnotationId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _gapped
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gapped", "gapped", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SecondaryStructure target = (SecondaryStructure) object;
- if (!target.hasGapped()) { return null; }
- return (target.getGapped() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SecondaryStructure target = (SecondaryStructure) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGapped();
- return;
- }
- target.setGapped( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _gapped
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _gapped
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_gapped", "gapped",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ if (!target.hasGapped())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _viewerState
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewerState", "viewerState", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SecondaryStructure target = (SecondaryStructure) object;
- return target.getViewerState();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SecondaryStructure target = (SecondaryStructure) object;
- target.setViewerState( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _viewerState
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return (target.getGapped() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGapped();
+ return;
+ }
+ target.setGapped(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _gapped
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _viewerState
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_viewerState", "viewerState",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getViewerState();
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setViewerState((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _viewerState
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.SecondaryStructure.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SecondaryStructure.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Sequence;
*
* @version $Revision$ $Date$
*/
-public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "Sequence";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _dsseqid
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getDsseqid();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.setDsseqid( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dsseqid
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _DBRefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getDBRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.addDBRef( (jalview.schemabinding.version2.DBRef) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Sequence target = (Sequence) object;
- target.removeAllDBRef();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.DBRef();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _DBRefList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- }
+public class SequenceDescriptor extends
+ jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
- //-----------/
- //- Methods -/
- //-----------/
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public SequenceDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "Sequence";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _dsseqid
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_dsseqid", "dsseqid",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Sequence target = (Sequence) object;
+ return target.getDsseqid();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Sequence target = (Sequence) object;
+ target.setDsseqid((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _dsseqid
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Sequence.class;
- }
+ // -- _DBRefList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.DBRef.class, "_DBRefList",
+ "DBRef", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Sequence target = (Sequence) object;
+ return target.getDBRef();
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Sequence target = (Sequence) object;
+ target.addDBRef((jalview.schemabinding.version2.DBRef) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Sequence target = (Sequence) object;
+ target.removeAllDBRef();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.DBRef();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _DBRefList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Sequence.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.SequenceSet;
*
* @version $Revision$ $Date$
*/
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSetDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "SequenceSet";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _gapChar
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getGapChar();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.setGapChar( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _gapChar
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class SequenceSetDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSetDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "SequenceSet";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _gapChar
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_gapChar", "gapChar",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getGapChar();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.setGapChar((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _datasetId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getDatasetId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.setDatasetId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _datasetId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _gapChar
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _datasetId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_datasetId", "datasetId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getDatasetId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.setDatasetId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _sequenceList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addSequence( (jalview.schemabinding.version2.Sequence) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- SequenceSet target = (SequenceSet) object;
- target.removeAllSequence();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Sequence();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _datasetId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _sequenceList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Sequence.class, "_sequenceList",
+ "Sequence", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getSequence();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.addSequence((jalview.schemabinding.version2.Sequence) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _annotationList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getAnnotation();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- SequenceSet target = (SequenceSet) object;
- target.removeAllAnnotation();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.Annotation();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.removeAllSequence();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _sequenceSetPropertiesList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getSequenceSetProperties();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- SequenceSet target = (SequenceSet) object;
- target.removeAllSequenceSetProperties();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.SequenceSetProperties();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceSetPropertiesList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Sequence();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequenceList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _annotationList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Annotation.class,
+ "_annotationList", "Annotation",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getAnnotation();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.addAnnotation((jalview.schemabinding.version2.Annotation) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _alcodonFrameList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getAlcodonFrame();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- SequenceSet target = (SequenceSet) object;
- target.removeAllAlcodonFrame();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.AlcodonFrame();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alcodonFrameList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.removeAllAnnotation();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Annotation();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _sequenceSetPropertiesList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SequenceSetProperties.class,
+ "_sequenceSetPropertiesList", "sequenceSetProperties",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getSequenceSetProperties();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.removeAllSequenceSetProperties();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SequenceSetProperties();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _sequenceSetPropertiesList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _alcodonFrameList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AlcodonFrame.class,
+ "_alcodonFrameList", "AlcodonFrame",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getAlcodonFrame();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.SequenceSet.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ SequenceSet target = (SequenceSet) object;
+ target.removeAllAlcodonFrame();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AlcodonFrame();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ // -- validation code for: _alcodonFrameList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SequenceSet.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.SequenceSetProperties;
*
* @version $Revision$ $Date$
*/
-public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSetPropertiesDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "sequenceSetProperties";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _key
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSetProperties target = (SequenceSetProperties) object;
- return target.getKey();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetProperties target = (SequenceSetProperties) object;
- target.setKey( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _key
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSetProperties target = (SequenceSetProperties) object;
- return target.getValue();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetProperties target = (SequenceSetProperties) object;
- target.setValue( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class SequenceSetPropertiesDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSetPropertiesDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "sequenceSetProperties";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _key
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_key", "key",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSetProperties target = (SequenceSetProperties) object;
+ return target.getKey();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSetProperties target = (SequenceSetProperties) object;
+ target.setKey((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _key
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _value
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_value", "value",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceSetProperties target = (SequenceSetProperties) object;
+ return target.getValue();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceSetProperties target = (SequenceSetProperties) object;
+ target.setValue((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.SequenceSetProperties.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _value
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SequenceSetProperties.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.SequenceType;
*
* @version $Revision$ $Date$
*/
-public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceTypeDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "SequenceType";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setDescription( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _sequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setSequence( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class SequenceTypeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceTypeDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "SequenceType";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceType target = (SequenceType) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_description", "description",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getDescription();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceType target = (SequenceType) object;
+ target.setDescription((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+ // -- _sequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_sequence", "sequence",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getSequence();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceType target = (SequenceType) object;
+ target.setSequence((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _sequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "name",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getName();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.SequenceType.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequenceType target = (SequenceType) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SequenceType.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Setting;
*
* @version $Revision$ $Date$
*/
-public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SettingDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "setting";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _type
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- target.setType( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _type
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class SettingDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SettingDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "setting";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _type
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_type", "type",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ return target.getType();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ target.setType((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasColour()) { return null; }
- return new java.lang.Integer(target.getColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _type
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_colour", "colour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasColour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _display
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasDisplay()) { return null; }
- return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // ignore null values for non optional primitives
- if (value == null) { return; }
-
- target.setDisplay( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _display
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _order
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasOrder()) { return null; }
- return new java.lang.Float(target.getOrder());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteOrder();
- return;
- }
- target.setOrder( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _order
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _display
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_display", "display",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasDisplay())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _mincolour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasMincolour()) { return null; }
- return new java.lang.Integer(target.getMincolour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMincolour();
- return;
- }
- target.setMincolour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mincolour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getDisplay() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.setDisplay(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasThreshold()) { return null; }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshold();
- return;
- }
- target.setThreshold( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _display
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _order
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_order", "order",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasOrder())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _threshstate
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasThreshstate()) { return null; }
- return new java.lang.Integer(target.getThreshstate());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshstate();
- return;
- }
- target.setThreshstate( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshstate
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Float(target.getOrder());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteOrder();
+ return;
+ }
+ target.setOrder(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _max
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasMax()) { return null; }
- return new java.lang.Float(target.getMax());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMax();
- return;
- }
- target.setMax( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _max
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _order
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _mincolour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_mincolour", "mincolour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasMincolour())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _min
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasMin()) { return null; }
- return new java.lang.Float(target.getMin());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMin();
- return;
- }
- target.setMin( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _min
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ return new java.lang.Integer(target.getMincolour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMincolour();
+ return;
+ }
+ target.setMincolour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colourByLabel
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasColourByLabel()) { return null; }
- return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColourByLabel();
- return;
- }
- target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourByLabel
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _mincolour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _autoScale
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Setting target = (Setting) object;
- if (!target.hasAutoScale()) { return null; }
- return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Setting target = (Setting) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAutoScale();
- return;
- }
- target.setAutoScale( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _autoScale
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Float(target.getThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshstate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_threshstate", "threshstate",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasThreshstate())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getThreshstate());
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshstate();
+ return;
+ }
+ target.setThreshstate(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _threshstate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _max
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_max", "max",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasMax())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getMax());
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Setting.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMax();
+ return;
+ }
+ target.setMax(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _max
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ // -- _min
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_min", "min",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasMin())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getMin());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMin();
+ return;
+ }
+ target.setMin(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _min
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
+ desc.setValidator(fieldValidator);
+ // -- _colourByLabel
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasColourByLabel())
+ {
+ return null;
+ }
+ return (target.getColourByLabel() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColourByLabel();
+ return;
+ }
+ target.setColourByLabel(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colourByLabel
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _autoScale
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_autoScale", "autoScale",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Setting target = (Setting) object;
+ if (!target.hasAutoScale())
+ {
+ return null;
+ }
+ return (target.getAutoScale() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Setting target = (Setting) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAutoScale();
+ return;
+ }
+ target.setAutoScale(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _autoScale
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Setting.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.StructureState;
*
* @version $Revision$ $Date$
*/
-public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public StructureStateDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "structureState";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- _content
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- return target.getContent();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- target.setContent( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- addFieldDescriptor(desc);
-
- //-- validation code for: _content
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize attribute descriptors
-
- //-- _visible
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasVisible()) { return null; }
- return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteVisible();
- return;
- }
- target.setVisible( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _visible
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+public class StructureStateDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public StructureStateDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "structureState";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- _content
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_content", "PCDATA",
+ org.exolab.castor.xml.NodeType.Text);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ return target.getContent();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ target.setContent((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _viewId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- return target.getViewId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- target.setViewId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _viewId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _content
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize attribute descriptors
+
+ // -- _visible
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_visible", "visible",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasVisible())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _alignwithAlignPanel
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasAlignwithAlignPanel()) { return null; }
- return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAlignwithAlignPanel();
- return;
- }
- target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignwithAlignPanel
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getVisible() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteVisible();
+ return;
+ }
+ target.setVisible(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colourwithAlignPanel
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasColourwithAlignPanel()) { return null; }
- return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColourwithAlignPanel();
- return;
- }
- target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourwithAlignPanel
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _visible
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _viewId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_viewId", "viewId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ return target.getViewId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ target.setViewId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _colourByJmol
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByJmol", "colourByJmol", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasColourByJmol()) { return null; }
- return (target.getColourByJmol() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColourByJmol();
- return;
- }
- target.setColourByJmol( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourByJmol
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _viewId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _alignwithAlignPanel
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_alignwithAlignPanel",
+ "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasAlignwithAlignPanel())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _type
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- target.setType( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _type
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAlignwithAlignPanel();
+ return;
+ }
+ target.setAlignwithAlignPanel(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _width
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasWidth()) { return null; }
- return new java.lang.Integer(target.getWidth());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteWidth();
- return;
- }
- target.setWidth( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _width
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _alignwithAlignPanel
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourwithAlignPanel
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_colourwithAlignPanel",
+ "colourwithAlignPanel",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasColourwithAlignPanel())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _height
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasHeight()) { return null; }
- return new java.lang.Integer(target.getHeight());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteHeight();
- return;
- }
- target.setHeight( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _height
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColourwithAlignPanel();
+ return;
+ }
+ target.setColourwithAlignPanel(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _xpos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasXpos()) { return null; }
- return new java.lang.Integer(target.getXpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteXpos();
- return;
- }
- target.setXpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _xpos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colourwithAlignPanel
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourByJmol
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_colourByJmol", "colourByJmol",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasColourByJmol())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _ypos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- StructureState target = (StructureState) object;
- if (!target.hasYpos()) { return null; }
- return new java.lang.Integer(target.getYpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- StructureState target = (StructureState) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteYpos();
- return;
- }
- target.setYpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ypos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getColourByJmol() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColourByJmol();
+ return;
+ }
+ target.setColourByJmol(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _colourByJmol
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _type
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_type", "type",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ return target.getType();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ target.setType((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _type
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasWidth())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getWidth());
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.StructureState.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.StructureState.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.ThresholdLine;
*
* @version $Revision$ $Date$
*/
-public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ThresholdLineDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "thresholdLine";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _label
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ThresholdLine target = (ThresholdLine) object;
- return target.getLabel();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ThresholdLine target = (ThresholdLine) object;
- target.setLabel( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _label
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class ThresholdLineDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public ThresholdLineDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "thresholdLine";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _label
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_label", "label",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ return target.getLabel();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ target.setLabel((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ThresholdLine target = (ThresholdLine) object;
- if (!target.hasValue()) { return null; }
- return new java.lang.Float(target.getValue());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ThresholdLine target = (ThresholdLine) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteValue();
- return;
- }
- target.setValue( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _label
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _value
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_value", "value",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ if (!target.hasValue())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _colour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ThresholdLine target = (ThresholdLine) object;
- if (!target.hasColour()) { return null; }
- return new java.lang.Integer(target.getColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ThresholdLine target = (ThresholdLine) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteColour();
- return;
- }
- target.setColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return new java.lang.Float(target.getValue());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteValue();
+ return;
+ }
+ target.setValue(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _value
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_colour", "colour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ if (!target.hasColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getColour());
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ ThresholdLine target = (ThresholdLine) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColour();
+ return;
+ }
+ target.setColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _colour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.ThresholdLine.class;
- }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.ThresholdLine.class;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Tree;
*
* @version $Revision$ $Date$
*/
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public TreeDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "tree";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _fontName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getFontName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setFontName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _fontSize
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFontSize()) { return null; }
- return new java.lang.Integer(target.getFontSize());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFontSize();
- return;
- }
- target.setFontSize( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontSize
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+public class TreeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public TreeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "tree";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _fontName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_fontName", "fontName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ return target.getFontName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ target.setFontName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _fontStyle
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFontStyle()) { return null; }
- return new java.lang.Integer(target.getFontStyle());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFontStyle();
- return;
- }
- target.setFontStyle( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontStyle
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fontName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _fontSize
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_fontSize", "fontSize",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFontSize())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasThreshold()) { return null; }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshold();
- return;
- }
- target.setThreshold( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ return new java.lang.Integer(target.getFontSize());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFontSize();
+ return;
+ }
+ target.setFontSize(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _showBootstrap
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasShowBootstrap()) { return null; }
- return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowBootstrap();
- return;
- }
- target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showBootstrap
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fontSize
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _fontStyle
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFontStyle())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _showDistances
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasShowDistances()) { return null; }
- return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowDistances();
- return;
- }
- target.setShowDistances( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showDistances
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Integer(target.getFontStyle());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFontStyle();
+ return;
+ }
+ target.setFontStyle(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _markUnlinked
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasMarkUnlinked()) { return null; }
- return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMarkUnlinked();
- return;
- }
- target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _markUnlinked
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fontStyle
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasThreshold())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _fitToWindow
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFitToWindow()) { return null; }
- return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFitToWindow();
- return;
- }
- target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fitToWindow
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ return new java.lang.Float(target.getThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _currentTree
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasCurrentTree()) { return null; }
- return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteCurrentTree();
- return;
- }
- target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _currentTree
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showBootstrap
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasShowBootstrap())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- super.setIdentity(desc);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IdValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();
- fieldValidator.setValidator(typeValidator);
+ return (target.getShowBootstrap() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowBootstrap();
+ return;
+ }
+ target.setShowBootstrap(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _width
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasWidth()) { return null; }
- return new java.lang.Integer(target.getWidth());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteWidth();
- return;
- }
- target.setWidth( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _width
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showBootstrap
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showDistances
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showDistances", "showDistances",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasShowDistances())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _height
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasHeight()) { return null; }
- return new java.lang.Integer(target.getHeight());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteHeight();
- return;
- }
- target.setHeight( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _height
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getShowDistances() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowDistances();
+ return;
+ }
+ target.setShowDistances(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _xpos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasXpos()) { return null; }
- return new java.lang.Integer(target.getXpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteXpos();
- return;
- }
- target.setXpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _xpos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showDistances
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _markUnlinked
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasMarkUnlinked())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _ypos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasYpos()) { return null; }
- return new java.lang.Integer(target.getYpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteYpos();
- return;
- }
- target.setYpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ypos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMarkUnlinked();
+ return;
+ }
+ target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setTitle( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _markUnlinked
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _fitToWindow
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFitToWindow())
+ {
+ return null;
}
- desc.setValidator(fieldValidator);
- //-- _newick
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getNewick();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setNewick( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _newick
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ return (target.getFitToWindow() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFitToWindow();
+ return;
+ }
+ target.setFitToWindow(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fitToWindow
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _currentTree
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_currentTree", "currentTree",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasCurrentTree())
+ {
+ return null;
+ }
+ return (target.getCurrentTree() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteCurrentTree();
+ return;
+ }
+ target.setCurrentTree(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _currentTree
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ super.setIdentity(desc);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ return target.getId();
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IdValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasWidth())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getWidth());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Tree.class;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ return target.getTitle();
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _newick
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_newick", "newick",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ return target.getNewick();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Tree target = (Tree) object;
+ target.setNewick((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _newick
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Tree.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import jalview.schemabinding.version2.UserColourScheme;
/**
* Class UserColourSchemeDescriptor.
*
* @version $Revision$ $Date$
*/
-public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColourSchemeDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "UserColourScheme";
- _elementDefinition = true;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.UserColourScheme.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+public class UserColourSchemeDescriptor
+ extends
+ jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public UserColourSchemeDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "UserColourScheme";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.UserColourScheme.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.UserColours;
*
* @version $Revision$ $Date$
*/
-public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public UserColoursDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "UserColours";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- UserColours target = (UserColours) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- UserColours target = (UserColours) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _userColourScheme
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- UserColours target = (UserColours) object;
- return target.getUserColourScheme();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- UserColours target = (UserColours) object;
- target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.UserColourScheme();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _userColourScheme
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
+public class UserColoursDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public UserColoursDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "UserColours";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ UserColours target = (UserColours) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ UserColours target = (UserColours) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.UserColours.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _userColourScheme
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.UserColourScheme.class,
+ "_userColourScheme", "UserColourScheme",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ UserColours target = (UserColours) object;
+ return target.getUserColourScheme();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ UserColours target = (UserColours) object;
+ target.setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.UserColourScheme();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _userColourScheme
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.UserColours.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.VAMSAS;
*
* @version $Revision$ $Date$
*/
-public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSASDescriptor() {
- super();
- _nsURI = "www.vamsas.ac.uk/jalview/version2";
- _xmlName = "VAMSAS";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VAMSAS target = (VAMSAS) object;
- return target.getTree();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.addTree( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- VAMSAS target = (VAMSAS) object;
- target.removeAllTree();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _treeList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class VAMSASDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VAMSASDescriptor()
+ {
+ super();
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";
+ _xmlName = "VAMSAS";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _treeList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_treeList", "Tree",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ VAMSAS target = (VAMSAS) object;
+ return target.getTree();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ VAMSAS target = (VAMSAS) object;
+ target.addTree((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _sequenceSetList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VAMSAS target = (VAMSAS) object;
- return target.getSequenceSet();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- VAMSAS target = (VAMSAS) object;
- target.removeAllSequenceSet();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.SequenceSet();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceSetList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ VAMSAS target = (VAMSAS) object;
+ target.removeAllTree();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _treeList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _sequenceSetList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SequenceSet.class,
+ "_sequenceSetList", "SequenceSet",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ VAMSAS target = (VAMSAS) object;
+ return target.getSequenceSet();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ VAMSAS target = (VAMSAS) object;
+ target.addSequenceSet((jalview.schemabinding.version2.SequenceSet) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ VAMSAS target = (VAMSAS) object;
+ target.removeAllSequenceSet();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SequenceSet();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _sequenceSetList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.VAMSAS.class;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.VAMSAS.class;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import jalview.schemabinding.version2.VamsasModel;
/**
* Class VamsasModelDescriptor.
*
* @version $Revision$ $Date$
*/
-public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VamsasModelDescriptor() {
- super();
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
- _nsURI = "www.jalview.org";
- _xmlName = "vamsasModel";
- _elementDefinition = true;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.VamsasModel.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+public class VamsasModelDescriptor extends
+ jalview.schemabinding.version2.descriptors.VAMSASDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VamsasModelDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "vamsasModel";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.VamsasModel.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Viewport;
*
* @version $Revision$ $Date$
*/
-public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ViewportDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "Viewport";
- _elementDefinition = true;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _conservationSelected
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasConservationSelected()) { return null; }
- return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteConservationSelected();
- return;
- }
- target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _conservationSelected
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _pidSelected
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasPidSelected()) { return null; }
- return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePidSelected();
- return;
- }
- target.setPidSelected( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pidSelected
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _bgColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getBgColour();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setBgColour( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _bgColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _consThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasConsThreshold()) { return null; }
- return new java.lang.Integer(target.getConsThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteConsThreshold();
- return;
- }
- target.setConsThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _consThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _pidThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasPidThreshold()) { return null; }
- return new java.lang.Integer(target.getPidThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePidThreshold();
- return;
- }
- target.setPidThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _pidThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setTitle( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _showFullId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowFullId()) { return null; }
- return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowFullId();
- return;
- }
- target.setShowFullId( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showFullId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _rightAlignIds
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasRightAlignIds()) { return null; }
- return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteRightAlignIds();
- return;
- }
- target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _rightAlignIds
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowText()) { return null; }
- return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowText();
- return;
- }
- target.setShowText( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showColourText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowColourText()) { return null; }
- return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowColourText();
- return;
- }
- target.setShowColourText( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showColourText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showUnconserved
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowUnconserved()) { return null; }
- return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowUnconserved();
- return;
- }
- target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showUnconserved
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showBoxes
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowBoxes()) { return null; }
- return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowBoxes();
- return;
- }
- target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showBoxes
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _wrapAlignment
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasWrapAlignment()) { return null; }
- return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteWrapAlignment();
- return;
- }
- target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _wrapAlignment
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _renderGaps
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasRenderGaps()) { return null; }
- return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteRenderGaps();
- return;
- }
- target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _renderGaps
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showSequenceFeatures
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowSequenceFeatures()) { return null; }
- return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowSequenceFeatures();
- return;
- }
- target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showSequenceFeatures
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showNPfeatureTooltip
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowNPfeatureTooltip()) { return null; }
- return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowNPfeatureTooltip();
- return;
- }
- target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showNPfeatureTooltip
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showDbRefTooltip
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowDbRefTooltip()) { return null; }
- return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowDbRefTooltip();
- return;
- }
- target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showDbRefTooltip
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _followHighlight
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFollowHighlight()) { return null; }
- return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFollowHighlight();
- return;
- }
- target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _followHighlight
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _followSelection
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFollowSelection()) { return null; }
- return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFollowSelection();
- return;
- }
- target.setFollowSelection( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _followSelection
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showAnnotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowAnnotation()) { return null; }
- return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowAnnotation();
- return;
- }
- target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showAnnotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _centreColumnLabels
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasCentreColumnLabels()) { return null; }
- return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteCentreColumnLabels();
- return;
- }
- target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _centreColumnLabels
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showGroupConservation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowGroupConservation()) { return null; }
- return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowGroupConservation();
- return;
- }
- target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showGroupConservation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showGroupConsensus
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowGroupConsensus()) { return null; }
- return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowGroupConsensus();
- return;
- }
- target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showGroupConsensus
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showConsensusHistogram
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowConsensusHistogram()) { return null; }
- return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowConsensusHistogram();
- return;
- }
- target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showConsensusHistogram
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _showSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowSequenceLogo()) { return null; }
- return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteShowSequenceLogo();
- return;
- }
- target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _showSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _normaliseSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_normaliseSequenceLogo", "normaliseSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasNormaliseSequenceLogo()) { return null; }
- return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteNormaliseSequenceLogo();
- return;
- }
- target.setNormaliseSequenceLogo( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _normaliseSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _ignoreGapsinConsensus
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasIgnoreGapsinConsensus()) { return null; }
- return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteIgnoreGapsinConsensus();
- return;
- }
- target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ignoreGapsinConsensus
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _startRes
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasStartRes()) { return null; }
- return new java.lang.Integer(target.getStartRes());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteStartRes();
- return;
- }
- target.setStartRes( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _startRes
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _startSeq
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasStartSeq()) { return null; }
- return new java.lang.Integer(target.getStartSeq());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteStartSeq();
- return;
- }
- target.setStartSeq( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _startSeq
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _fontName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getFontName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setFontName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _fontSize
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFontSize()) { return null; }
- return new java.lang.Integer(target.getFontSize());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFontSize();
- return;
- }
- target.setFontSize( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontSize
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _fontStyle
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFontStyle()) { return null; }
- return new java.lang.Integer(target.getFontStyle());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteFontStyle();
- return;
- }
- target.setFontStyle( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _fontStyle
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _scaleProteinAsCdna
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleProteinAsCdna", "scaleProteinAsCdna", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasScaleProteinAsCdna()) { return null; }
- return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteScaleProteinAsCdna();
- return;
- }
- target.setScaleProteinAsCdna( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _scaleProteinAsCdna
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _viewName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getViewName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setViewName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _viewName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _sequenceSetId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getSequenceSetId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setSequenceSetId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceSetId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _gatheredViews
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasGatheredViews()) { return null; }
- return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteGatheredViews();
- return;
- }
- target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _gatheredViews
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _textCol1
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextCol1()) { return null; }
- return new java.lang.Integer(target.getTextCol1());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextCol1();
- return;
- }
- target.setTextCol1( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textCol1
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _textCol2
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextCol2()) { return null; }
- return new java.lang.Integer(target.getTextCol2());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextCol2();
- return;
- }
- target.setTextCol2( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textCol2
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _textColThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextColThreshold()) { return null; }
- return new java.lang.Integer(target.getTextColThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteTextColThreshold();
- return;
- }
- target.setTextColThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _textColThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- super.setIdentity(desc);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IdValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _complementId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_complementId", "complementId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getComplementId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setComplementId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _complementId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _width
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasWidth()) { return null; }
- return new java.lang.Integer(target.getWidth());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteWidth();
- return;
- }
- target.setWidth( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _width
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _height
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasHeight()) { return null; }
- return new java.lang.Integer(target.getHeight());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteHeight();
- return;
- }
- target.setHeight( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _height
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _xpos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasXpos()) { return null; }
- return new java.lang.Integer(target.getXpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteXpos();
- return;
- }
- target.setXpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _xpos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _ypos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasYpos()) { return null; }
- return new java.lang.Integer(target.getYpos());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteYpos();
- return;
- }
- target.setYpos( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _ypos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _annotationColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getAnnotationColours();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.AnnotationColours();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _hiddenColumnsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getHiddenColumns();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Viewport target = (Viewport) object;
- target.removeAllHiddenColumns();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.HiddenColumns();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _hiddenColumnsList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _calcIdParamList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.CalcIdParam.class, "_calcIdParamList", "calcIdParam", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getCalcIdParam();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Viewport target = (Viewport) object;
- target.addCalcIdParam( (jalview.schemabinding.version2.CalcIdParam) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Viewport target = (Viewport) object;
- target.removeAllCalcIdParam();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new jalview.schemabinding.version2.CalcIdParam();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _calcIdParamList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
+public class ViewportDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public ViewportDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "Viewport";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _conservationSelected
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_conservationSelected",
+ "conservationSelected",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasConservationSelected())
+ {
+ return null;
+ }
+ return (target.getConservationSelected() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteConservationSelected();
+ return;
+ }
+ target.setConservationSelected(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _conservationSelected
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pidSelected
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_pidSelected", "pidSelected",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasPidSelected())
+ {
+ return null;
+ }
+ return (target.getPidSelected() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePidSelected();
+ return;
+ }
+ target.setPidSelected(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pidSelected
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _bgColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_bgColour", "bgColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getBgColour();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setBgColour((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _bgColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _consThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasConsThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getConsThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteConsThreshold();
+ return;
+ }
+ target.setConsThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _consThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pidThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasPidThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getPidThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePidThreshold();
+ return;
+ }
+ target.setPidThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pidThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getTitle();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showFullId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showFullId", "showFullId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowFullId())
+ {
+ return null;
+ }
+ return (target.getShowFullId() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowFullId();
+ return;
+ }
+ target.setShowFullId(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showFullId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _rightAlignIds
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasRightAlignIds())
+ {
+ return null;
+ }
+ return (target.getRightAlignIds() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteRightAlignIds();
+ return;
+ }
+ target.setRightAlignIds(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rightAlignIds
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showText", "showText",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowText())
+ {
+ return null;
+ }
+ return (target.getShowText() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowText();
+ return;
+ }
+ target.setShowText(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showColourText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showColourText", "showColourText",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowColourText())
+ {
+ return null;
+ }
+ return (target.getShowColourText() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowColourText();
+ return;
+ }
+ target.setShowColourText(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showColourText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showUnconserved
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowUnconserved())
+ {
+ return null;
+ }
+ return (target.getShowUnconserved() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowUnconserved();
+ return;
+ }
+ target.setShowUnconserved(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showUnconserved
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showBoxes
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showBoxes", "showBoxes",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowBoxes())
+ {
+ return null;
+ }
+ return (target.getShowBoxes() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowBoxes();
+ return;
+ }
+ target.setShowBoxes(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showBoxes
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _wrapAlignment
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasWrapAlignment())
+ {
+ return null;
+ }
+ return (target.getWrapAlignment() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWrapAlignment();
+ return;
+ }
+ target.setWrapAlignment(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _wrapAlignment
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _renderGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_renderGaps", "renderGaps",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasRenderGaps())
+ {
+ return null;
+ }
+ return (target.getRenderGaps() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteRenderGaps();
+ return;
+ }
+ target.setRenderGaps(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _renderGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showSequenceFeatures
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showSequenceFeatures",
+ "showSequenceFeatures",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowSequenceFeatures())
+ {
+ return null;
+ }
+ return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowSequenceFeatures();
+ return;
+ }
+ target.setShowSequenceFeatures(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showSequenceFeatures
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showNPfeatureTooltip
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showNPfeatureTooltip",
+ "showNPfeatureTooltip",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowNPfeatureTooltip())
+ {
+ return null;
+ }
+ return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowNPfeatureTooltip();
+ return;
+ }
+ target.setShowNPfeatureTooltip(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showNPfeatureTooltip
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showDbRefTooltip
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showDbRefTooltip",
+ "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowDbRefTooltip())
+ {
+ return null;
+ }
+ return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowDbRefTooltip();
+ return;
+ }
+ target.setShowDbRefTooltip(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showDbRefTooltip
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _followHighlight
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_followHighlight", "followHighlight",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFollowHighlight())
+ {
+ return null;
+ }
+ return (target.getFollowHighlight() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFollowHighlight();
+ return;
+ }
+ target.setFollowHighlight(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _followHighlight
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _followSelection
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_followSelection", "followSelection",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFollowSelection())
+ {
+ return null;
+ }
+ return (target.getFollowSelection() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFollowSelection();
+ return;
+ }
+ target.setFollowSelection(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _followSelection
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showAnnotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowAnnotation())
+ {
+ return null;
+ }
+ return (target.getShowAnnotation() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowAnnotation();
+ return;
+ }
+ target.setShowAnnotation(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showAnnotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _centreColumnLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_centreColumnLabels",
+ "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasCentreColumnLabels())
+ {
+ return null;
+ }
+ return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteCentreColumnLabels();
+ return;
+ }
+ target.setCentreColumnLabels(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _centreColumnLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showGroupConservation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showGroupConservation",
+ "showGroupConservation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowGroupConservation())
+ {
+ return null;
+ }
+ return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowGroupConservation();
+ return;
+ }
+ target.setShowGroupConservation(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showGroupConservation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showGroupConsensus
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showGroupConsensus",
+ "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowGroupConsensus())
+ {
+ return null;
+ }
+ return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowGroupConsensus();
+ return;
+ }
+ target.setShowGroupConsensus(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showGroupConsensus
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _showConsensusHistogram
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showConsensusHistogram",
+ "showConsensusHistogram",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowConsensusHistogram())
+ {
+ return null;
+ }
+ return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowConsensusHistogram();
+ return;
+ }
+ target.setShowConsensusHistogram(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showConsensusHistogram
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showSequenceLogo",
+ "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowSequenceLogo())
+ {
+ return null;
+ }
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowSequenceLogo();
+ return;
+ }
+ target.setShowSequenceLogo(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _normaliseSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_normaliseSequenceLogo",
+ "normaliseSequenceLogo",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasNormaliseSequenceLogo())
+ {
+ return null;
+ }
+ return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteNormaliseSequenceLogo();
+ return;
+ }
+ target.setNormaliseSequenceLogo(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _normaliseSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _ignoreGapsinConsensus
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",
+ "ignoreGapsinConsensus",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasIgnoreGapsinConsensus())
+ {
+ return null;
+ }
+ return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIgnoreGapsinConsensus();
+ return;
+ }
+ target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ignoreGapsinConsensus
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _startRes
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_startRes", "startRes",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasStartRes())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getStartRes());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteStartRes();
+ return;
+ }
+ target.setStartRes(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _startRes
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _startSeq
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_startSeq", "startSeq",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasStartSeq())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getStartSeq());
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteStartSeq();
+ return;
+ }
+ target.setStartSeq(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-----------/
- //- Methods -/
- //-----------/
+ // -- validation code for: _startSeq
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _fontName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_fontName", "fontName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getFontName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setFontName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fontName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _fontSize
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_fontSize", "fontSize",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFontSize())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getFontSize());
+ }
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFontSize();
+ return;
+ }
+ target.setFontSize(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _fontSize
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _fontStyle
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFontStyle())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getFontStyle());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteFontStyle();
+ return;
+ }
+ target.setFontStyle(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.Viewport.class;
+ // -- validation code for: _fontStyle
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _scaleProteinAsCdna
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_scaleProteinAsCdna",
+ "scaleProteinAsCdna", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasScaleProteinAsCdna())
+ {
+ return null;
+ }
+ return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScaleProteinAsCdna();
+ return;
+ }
+ target.setScaleProteinAsCdna(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scaleProteinAsCdna
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _viewName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_viewName", "viewName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getViewName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setViewName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _viewName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _sequenceSetId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_sequenceSetId", "sequenceSetId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getSequenceSetId();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setSequenceSetId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequenceSetId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _gatheredViews
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasGatheredViews())
+ {
+ return null;
+ }
+ return (target.getGatheredViews() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteGatheredViews();
+ return;
+ }
+ target.setGatheredViews(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _gatheredViews
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
+ desc.setValidator(fieldValidator);
+ // -- _textCol1
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textCol1", "textCol1",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextCol1())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getTextCol1());
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextCol1();
+ return;
+ }
+ target.setTextCol1(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _textCol1
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
+ desc.setValidator(fieldValidator);
+ // -- _textCol2
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textCol2", "textCol2",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextCol2())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getTextCol2());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextCol2();
+ return;
+ }
+ target.setTextCol2(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _textCol2
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _textColThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_textColThreshold",
+ "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextColThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getTextColThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteTextColThreshold();
+ return;
+ }
+ target.setTextColThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _textColThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ super.setIdentity(desc);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IdValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _complementId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_complementId", "complementId",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getComplementId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setComplementId((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _complementId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasWidth())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getWidth());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _annotationColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ "_annotationColours", "AnnotationColours",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getAnnotationColours();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AnnotationColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _hiddenColumnsList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.HiddenColumns.class,
+ "_hiddenColumnsList", "hiddenColumns",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getHiddenColumns();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.removeAllHiddenColumns();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.HiddenColumns();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _hiddenColumnsList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _calcIdParamList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.CalcIdParam.class,
+ "_calcIdParamList", "calcIdParam",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getCalcIdParam();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.addCalcIdParam((jalview.schemabinding.version2.CalcIdParam) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ Viewport target = (Viewport) object;
+ target.removeAllCalcIdParam();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.CalcIdParam();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _calcIdParamList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Viewport.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.WebServiceParameterSet;
*
* @version $Revision$ $Date$
*/
-public class WebServiceParameterSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public WebServiceParameterSetDescriptor() {
- super();
- _nsURI = "www.jalview.org/xml/wsparamset";
- _xmlName = "WebServiceParameterSet";
- _elementDefinition = false;
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setName( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setVersion( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setDescription( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _serviceURLList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_serviceURLList", "serviceURL", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getServiceURL();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.addServiceURL( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.removeAllServiceURL();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _serviceURLList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _parameters
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_parameters", "parameters", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getParameters();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setParameters( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _parameters
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+public class WebServiceParameterSetDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public WebServiceParameterSetDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org/xml/wsparamset";
+ _xmlName = "WebServiceParameterSet";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_name", "name",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+ // -- _version
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_version", "Version",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getVersion();
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setVersion((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
return null;
- }
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _version
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_description", "description",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getDescription();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.WebServiceParameterSet.class;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setDescription((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
+ // -- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ // -- _serviceURLList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_serviceURLList", "serviceURL",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getServiceURL();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.addServiceURL((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.removeAllServiceURL();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _serviceURLList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _parameters
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_parameters", "parameters",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getParameters();
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setParameters((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _parameters
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.WebServiceParameterSet.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
private boolean predefinedColours = false;
private boolean seqAssociated = false;
+
/**
* false if the scheme was constructed without a minColour and maxColour used
* to decide if existing colours should be taken from annotation elements when
* they exist
*/
private boolean noGradient = false;
+
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
: alignment.getContext();
- boolean f = true,rna=false;
+ boolean f = true, rna = false;
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
}
float aamin = 0f, aamax = 0f;
+
public String getAnnotation()
{
return annotation.label;
public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
- : this.annotation);
+ AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+ .get(seq) : this.annotation);
if (annotation == null)
{
return currentColour;
return new Color(dr, dg, db);
}
+
public boolean isPredefinedColours()
{
return predefinedColours;
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
*/
package jalview.schemes;
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Map;
+
public interface ColourSchemeI
{
/**
*/
package jalview.schemes;
-import java.awt.*;
-import java.util.Hashtable;
-
import jalview.datamodel.AlignmentAnnotation;
+import java.awt.Color;
+import java.util.Hashtable;
+
/**
* Became RNAHelicesColour.java. Placeholder for true covariation color scheme
*
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
public class HelixColourScheme extends ScoreColourScheme
{
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* Class is based off of NucleotideColourScheme
public class RNAHelicesColour extends ResidueColourScheme
{
-
/**
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
return getClass().newInstance();
} catch (Exception q)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_duplicate_colour_scheme", new String[]{getClass().getName()}), q);
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_duplicate_colour_scheme",
+ new String[] { getClass().getName() }), q);
}
}
}
aa2Triplet.put("v", "VAL");
}
- public static final String[] aa =
- { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
- "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " };
+ public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
+ "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
+ "Z", "X", "_", "*", ".", " " };
public static final Color midBlue = new Color(100, 100, 255);
scaleColours.addElement(Color.white);
}
- public static final Color[] taylor =
- { new Color(204, 255, 0), // A Greenish-yellowy-yellow
+ public static final Color[] taylor = { new Color(204, 255, 0), // A
+ // Greenish-yellowy-yellow
new Color(0, 0, 255), // R Blueish-bluey-blue
new Color(204, 0, 255), // N Blueish-reddy-blue
new Color(255, 0, 0), // D Reddish-reddy-red
Color.white // .
};
- public static final Color[] nucleotide =
- { new Color(100, 247, 63), // A
+ public static final Color[] nucleotide = { new Color(100, 247, 63), // A
new Color(255, 179, 64), // C
new Color(235, 65, 60), // G
new Color(60, 136, 238), // T
};
// Added for PurinePyrimidineColourScheme
- public static final Color[] purinepyrimidine =
- { new Color(255, 131, 250), // A, G, R purines purplish/orchid
+ public static final Color[] purinepyrimidine = {
+ new Color(255, 131, 250), // A, G, R purines purplish/orchid
new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
Color.white, // all other nucleotides
Color.white // Gap
};
// Zappo
- public static final Color[] zappo =
- { Color.pink, // A
+ public static final Color[] zappo = { Color.pink, // A
midBlue, // R
Color.green, // N
Color.red, // D
};
// Dunno where I got these numbers from
- public static final double[] hyd2 =
- { 0.62, // A
+ public static final double[] hyd2 = { 0.62, // A
0.29, // R
-0.90, // N
-0.74, // D
0.0 // X
};
- public static final double[] helix =
- { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
- 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
+ public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70,
+ 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77,
+ 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
public static final double helixmin = 0.57;
public static final double helixmax = 1.51;
- public static final double[] strand =
- { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
- 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
+ public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
+ 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
+ 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
public static final double strandmin = 0.37;
public static final double strandmax = 1.7;
- public static final double[] turn =
- { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
- 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0,
- 0 };
+ public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
+ 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
+ 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
public static final double turnmin = 0.47;
public static final double turnmax = 1.56;
- public static final double[] buried =
- { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
- 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00 };
+ public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3,
+ 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5,
+ 2.9, 0.4, 0.3, 1.358, 0.00 };
public static final double buriedmin = 0.05;
// This is hydropathy index
// Kyte, J., and Doolittle, R.F., J. Mol. Biol.
// 1157, 105-132, 1982
- public static final double[] hyd =
- { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9,
- 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
+ public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
+ -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
+ -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
public static final double hydmax = 4.5;
// public static final double hydmax = 1.38;
// public static final double hydmin = -2.53;
- private static final int[][] BLOSUM62 =
- {
+ private static final int[][] BLOSUM62 = {
{ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-2, 0, -2, -1, 0, -4 },
{ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
{ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-4, -4, -4, -4, -4, -4, 1 }, };
- static final int[][] PAM250 =
- {
+ static final int[][] PAM250 = {
{ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
0, 0, 0, 0, -8 },
{ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
// treats T and U identically. R and Y weak equivalence with AG and CTU.
// N matches any other base weakly
//
- static final int[][] DNA =
- {
- { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
+ static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
{ -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
{ -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
{ -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
}
- public static final Color[] pidColours =
- { midBlue, new Color(153, 153, 255),
+ public static final Color[] pidColours = { midBlue,
+ new Color(153, 153, 255),
// Color.lightGray,
new Color(204, 204, 255), };
- public static final float[] pidThresholds =
- { 80, 60, 40, };
+ public static final float[] pidThresholds = { 80, 60, 40, };
public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
/*
* Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
*/
- ambiguityCodes.put("R", new String[]
- { "A", "G" });
- ambiguityCodes.put("Y", new String[]
- { "T", "C" });
- ambiguityCodes.put("W", new String[]
- { "A", "T" });
- ambiguityCodes.put("S", new String[]
- { "G", "C" });
- ambiguityCodes.put("M", new String[]
- { "A", "C" });
- ambiguityCodes.put("K", new String[]
- { "G", "T" });
- ambiguityCodes.put("H", new String[]
- { "A", "T", "C" });
- ambiguityCodes.put("B", new String[]
- { "G", "T", "C" });
- ambiguityCodes.put("V", new String[]
- { "G", "A", "C" });
- ambiguityCodes.put("D", new String[]
- { "G", "A", "T" });
- ambiguityCodes.put("N", new String[]
- { "G", "A", "T", "C" });
+ ambiguityCodes.put("R", new String[] { "A", "G" });
+ ambiguityCodes.put("Y", new String[] { "T", "C" });
+ ambiguityCodes.put("W", new String[] { "A", "T" });
+ ambiguityCodes.put("S", new String[] { "G", "C" });
+ ambiguityCodes.put("M", new String[] { "A", "C" });
+ ambiguityCodes.put("K", new String[] { "G", "T" });
+ ambiguityCodes.put("H", new String[] { "A", "T", "C" });
+ ambiguityCodes.put("B", new String[] { "G", "T", "C" });
+ ambiguityCodes.put("V", new String[] { "G", "A", "C" });
+ ambiguityCodes.put("D", new String[] { "G", "A", "T" });
+ ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
// Now build codon translation table
codonHash2.put("AAA", "K");
}
else
{
- acodon[i] = new String[]
- {};
+ acodon[i] = new String[] {};
}
}
// enumerate all combinations and test for veracity of translation
if (acodon[ipos].length == 0 || tpos[ipos] < 0)
{
_acodon += codon.charAt(ipos);
- allres[ipos] = new char[]
- { codon.charAt(ipos) };
+ allres[ipos] = new char[] { codon.charAt(ipos) };
}
else
{
propMatrixF[i][j] = 0;
propMatrixPos[i][j] = 0;
propMatrixEpos[i][j] = 0;
- for (Enumeration<String> en = propHash.keys(); en
- .hasMoreElements();)
+ for (Enumeration<String> en = propHash.keys(); en.hasMoreElements();)
{
String ph = en.nextElement();
Map<String, Integer> pph = (Map<String, Integer>) propHash
}
System.out.println("};");
}
+
// to here
/**
result.add(nuc);
}
}
- } else {
+ }
+ else
+ {
/*
* Peptide
*/
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
*/
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
public class TCoffeeColourScheme extends ResidueColourScheme
{
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
*/
package jalview.schemes;
-import java.awt.Color;
-import java.util.Map;
-import java.util.StringTokenizer;
-
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
public class UserColourScheme extends ResidueColourScheme
{
Color[] lowerCaseColours;
import jalview.datamodel.SequenceI;
-
public interface SequenceListener
{
// TODO remove this? never called on SequenceListener type
*/
package jalview.structure;
-import java.util.List;
-
import jalview.datamodel.SequenceI;
+import java.util.List;
+
public interface StructureListener
{
/**
resNum = tmp.resNumber;
if (tmp.alignmentMapping >= -1)
{
- // TODO (JAL-1836) address root cause: negative residue no in PDB file
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
}
{
results = MappingUtils.buildSearchResults(seq, index,
seqmappings);
- }
+ }
if (handlingVamsasMo)
{
results.addResult(seq, index, index);
package jalview.structures.models;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.util.Comparison;
import jalview.util.MessageManager;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
/**
*
* A base class to hold common function for protein structure model binding.
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
- * @param viewerName TODO
+ *
+ * @param viewerName
+ * TODO
* @param verbose
*
* @return
public String getViewerTitle(String viewerName, boolean verbose)
{
if (getSequence() == null || getSequence().length < 1
- || getPdbCount() < 1
- || getSequence()[0].length < 1)
+ || getPdbCount() < 1 || getSequence()[0].length < 1)
{
return ("Jalview " + viewerName + " Window");
}
StringBuilder title = new StringBuilder(64);
final PDBEntry pdbEntry = getPdbEntry(0);
title.append(viewerName + " view for " + getSequence()[0][0].getName()
- + ":"
- + pdbEntry.getId());
-
+ + ":" + pdbEntry.getId());
+
if (verbose)
{
if (pdbEntry.getProperty() != null)
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_no_pdbentry_from_index",
- new Object[]
- { Integer.valueOf(pe).toString() }));
+ new Object[] { Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
List<SequenceI> s = new ArrayList<SequenceI>();
*
* @returns the pdb entries added to the current set.
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
- String[][] chns)
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
{
List<PDBEntry> v = new ArrayList<PDBEntry>();
List<int[]> rtn = new ArrayList<int[]>();
int r = v.indexOf(pdbe[i]);
if (r == -1 || r >= getPdbCount())
{
- rtn.add(new int[]
- { v.size(), i });
+ rtn.add(new int[] { v.size(), i });
v.add(pdbe[i]);
}
else
//
// RJHM van den Bergh , rvdb@comweb.nl
-import java.io.*;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.GraphicsEnvironment;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.IOException;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
public class AWTConsole extends WindowAdapter implements WindowListener,
ActionListener, Runnable
} catch (InterruptedException ie)
{
}
- throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
+ throw new NullPointerException(
+ MessageManager.getString("exception.application_test_npe"));
}
}
*/
package jalview.util;
-import java.io.*;
-import java.lang.reflect.*;
+import java.io.File;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
/**
* BrowserLauncher is a class that provides one static method, openURL, which
aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
aeTargetConstructor = aeTargetClass
- .getDeclaredConstructor(new Class[]
- { int.class });
+ .getDeclaredConstructor(new Class[] { int.class });
appleEventConstructor = appleEventClass
- .getDeclaredConstructor(new Class[]
- { int.class, int.class, aeTargetClass, int.class, int.class });
- aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
- { String.class });
+ .getDeclaredConstructor(new Class[] { int.class, int.class,
+ aeTargetClass, int.class, int.class });
+ aeDescConstructor = aeDescClass
+ .getDeclaredConstructor(new Class[] { String.class });
makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
- new Class[]
- { String.class });
+ new Class[] { String.class });
putParameter = appleEventClass.getDeclaredMethod("putParameter",
- new Class[]
- { int.class, aeDescClass });
+ new Class[] { int.class, aeDescClass });
sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
- new Class[]
- {});
+ new Class[] {});
Field keyDirectObjectField = aeClass
.getDeclaredField("keyDirectObject");
.getDeclaredField("kSystemFolderType");
kSystemFolderType = systemFolderField.get(null);
findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
- new Class[]
- { mrjOSTypeClass });
+ new Class[] { mrjOSTypeClass });
getFileCreator = mrjFileUtilsClass.getDeclaredMethod(
- "getFileCreator", new Class[]
- { File.class });
+ "getFileCreator", new Class[] { File.class });
getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
- new Class[]
- { File.class });
+ new Class[] { File.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
try
{
Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
- Constructor constructor = linker.getConstructor(new Class[]
- { Class.class });
- linkage = constructor.newInstance(new Object[]
- { BrowserLauncher.class });
+ Constructor constructor = linker
+ .getConstructor(new Class[] { Class.class });
+ linkage = constructor
+ .newInstance(new Object[] { BrowserLauncher.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
{
mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
- new Class[]
- { String.class });
+ new Class[] { String.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
try
{
Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
- new Object[]
- { FINDER_CREATOR });
- Object aeTarget = aeTargetConstructor.newInstance(new Object[]
- { finderCreatorCode });
- Integer gurlType = (Integer) makeOSType.invoke(null, new Object[]
- { GURL_EVENT });
- Object appleEvent = appleEventConstructor.newInstance(new Object[]
- { gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+ new Object[] { FINDER_CREATOR });
+ Object aeTarget = aeTargetConstructor
+ .newInstance(new Object[] { finderCreatorCode });
+ Integer gurlType = (Integer) makeOSType.invoke(null,
+ new Object[] { GURL_EVENT });
+ Object appleEvent = appleEventConstructor.newInstance(new Object[] {
+ gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
kAnyTransactionID });
// Don't set browser = appleEvent because then the next time we call
try
{
- systemFolder = (File) findFolder.invoke(null, new Object[]
- { kSystemFolderType });
+ systemFolder = (File) findFolder.invoke(null,
+ new Object[] { kSystemFolderType });
} catch (IllegalArgumentException iare)
{
browser = null;
// applications being picked up on certain Mac OS 9 systems,
// especially German ones, and sending a GURL event to those
// applications results in a logout under Multiple Users.
- Object fileType = getFileType.invoke(null, new Object[]
- { file });
+ Object fileType = getFileType.invoke(null, new Object[] { file });
if (FINDER_TYPE.equals(fileType.toString()))
{
- Object fileCreator = getFileCreator.invoke(null, new Object[]
- { file });
+ Object fileCreator = getFileCreator.invoke(null,
+ new Object[] { file });
if (FINDER_CREATOR.equals(fileCreator.toString()))
{
{
if (!loadedWithoutErrors)
{
- throw new IOException(MessageManager.formatMessage("exception.browser_not_found", new String[]{errorMessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.browser_not_found", new String[] { errorMessage }));
}
Object browser = locateBrowser();
if (browser == null)
{
- throw new IOException(MessageManager.formatMessage("exception.browser_unable_to_locate", new String[]{errorMessage}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.browser_unable_to_locate",
+ new String[] { errorMessage }));
}
switch (jvm)
try
{
- aeDesc = aeDescConstructor.newInstance(new Object[]
- { url });
- putParameter.invoke(browser, new Object[]
- { keyDirectObject, aeDesc });
- sendNoReply.invoke(browser, new Object[]
- {});
+ aeDesc = aeDescConstructor.newInstance(new Object[] { url });
+ putParameter.invoke(browser,
+ new Object[] { keyDirectObject, aeDesc });
+ sendNoReply.invoke(browser, new Object[] {});
} catch (InvocationTargetException ite)
{
- throw new IOException(MessageManager.formatMessage("exception.invocation_target_exception_creating_aedesc", new String[]{ite.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.invocation_target_exception_creating_aedesc",
+ new String[] { ite.getMessage() }));
} catch (IllegalAccessException iae)
{
- throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{iae.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.illegal_access_building_apple_evt", new String[]
+ { iae.getMessage() }));
} catch (InstantiationException ie)
{
- throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{ie.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.illegal_access_building_apple_evt", new String[]
+ { ie.getMessage() }));
} finally
{
aeDesc = null; // Encourage it to get disposed if it was created
break;
case MRJ_2_1:
- Runtime.getRuntime().exec(new String[]
- { (String) browser, url });
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });
break;
if (result == 0)
{
- int[] selectionStart = new int[]
- { 0 };
+ int[] selectionStart = new int[] { 0 };
byte[] urlBytes = url.getBytes();
- int[] selectionEnd = new int[]
- { urlBytes.length };
- result = ICLaunchURL(instance[0], new byte[]
- { 0 }, urlBytes, urlBytes.length, selectionStart, selectionEnd);
+ int[] selectionEnd = new int[] { urlBytes.length };
+ result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
+ urlBytes.length, selectionStart, selectionEnd);
if (result == 0)
{
}
else
{
- throw new IOException(MessageManager.formatMessage("exception.unable_to_launch_url", new String[]{Integer.valueOf(result).toString()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unable_to_launch_url", new String[] { Integer
+ .valueOf(result).toString() }));
}
}
else
{
- throw new IOException(MessageManager.formatMessage("exception.unable_to_create_internet_config", new String[]{Integer.valueOf(result).toString()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unable_to_create_internet_config",
+ new String[] { Integer.valueOf(result).toString() }));
}
break;
try
{
- openURL.invoke(null, new Object[]
- { url });
+ openURL.invoke(null, new Object[] { url });
} catch (InvocationTargetException ite)
{
- throw new IOException(MessageManager.formatMessage("exception.invocation_target_calling_url", new String[]{ite.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.invocation_target_calling_url",
+ new String[] { ite.getMessage() }));
} catch (IllegalAccessException iae)
{
- throw new IOException(MessageManager.formatMessage("exception.illegal_access_calling_url", new String[]{iae.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.illegal_access_calling_url",
+ new String[] { iae.getMessage() }));
}
break;
// Add quotes around the URL to allow ampersands and other special
// characters to work.
Process process = Runtime.getRuntime().exec(
- new String[]
- { (String) browser, FIRST_WINDOWS_PARAMETER,
+ new String[] { (String) browser, FIRST_WINDOWS_PARAMETER,
SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
'"' + url + '"' });
process.exitValue();
} catch (InterruptedException ie)
{
- throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.interrupted_launching_browser",
+ new String[] { ie.getMessage() }));
}
break;
* NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END);
*/
process = Runtime.getRuntime().exec(
- new String[]
- {
+ new String[] {
(String) browser,
NETSCAPE_REMOTE_PARAMETER,
if (exitCode != 0)
{ // if Netscape was not open
- Runtime.getRuntime().exec(new String[]
- { (String) browser, url });
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });
}
} catch (InterruptedException ie)
{
- throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.interrupted_launching_browser",
+ new String[] { ie.getMessage() }));
}
break;
// This should never occur, but if it does, we'll try the simplest thing
// possible
- Runtime.getRuntime().exec(new String[]
- { (String) browser, url });
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });
break;
}
*/
package jalview.util;
+import jalview.datamodel.SequenceI;
+
import java.util.ArrayList;
import java.util.List;
-import jalview.datamodel.SequenceI;
-
/**
* Assorted methods for analysing or comparing sequences.
*/
private static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[]
- { GAP_SPACE, GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(new char[] { GAP_SPACE,
+ GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
List<SequenceI> flattened = new ArrayList<SequenceI>();
for (SequenceI[] ss : seqs)
{
- for (SequenceI s : ss) {
- flattened.add(s);
+ for (SequenceI s : ss)
+ {
+ flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened.size()]);
+ final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
+ .size()]);
return isNucleotide(oneDArray);
}
}
{
return false;
}
- String coordsys = dasCoordinateSystemsLookup.get(string
- .toLowerCase());
+ String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
return coordsys == null ? false : coordsys.equals(dBRefEntry
.getSource());
}
{
return null;
}
- String canonical = canonicalSourceNameLookup.get(source
- .toLowerCase());
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
return canonical == null ? source : canonical;
}
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
- if (chaincode==null)
+ if (chaincode == null)
{
chaincode = " ";
}
pdbr.setChainCode(chaincode);
// pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
- } else {
- System.err.println("Malformed PDB DR line:"+acn);
+ }
+ else
+ {
+ System.err.println("Malformed PDB DR line:" + acn);
}
}
else
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
-import java.util.Vector;
public class GroupUrlLink
{
{
if (tokens == null)
{
- tokens = new String[]
- { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
+ tokens = new String[] { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
}
}
Hashtable rstrings = new Hashtable();
rstrings.put(tokens[0], idstrings);
rstrings.put(tokens[1], seqstrings);
- rstrings.put(tokens[2], new String[]
- { dsstring });
+ rstrings.put(tokens[2], new String[] { dsstring });
if (idstrings.length != seqstrings.length)
{
- throw new Error(MessageManager.getString("error.idstring_seqstrings_only_one_per_sequence"));
+ throw new Error(
+ MessageManager
+ .getString("error.idstring_seqstrings_only_one_per_sequence"));
}
return rstrings;
}
Object[] stubs = makeUrlsIf(false, rstrings, b);
if (stubs != null)
{
- return new Object[]
- { stubs[0], stubs[1], rstrings, new boolean[]
- { b } };
+ return new Object[] { stubs[0], stubs[1], rstrings,
+ new boolean[] { b } };
}
// TODO Auto-generated method stub
return null;
{
if (maxs != idseq[i].length)
{
- throw new Error(MessageManager.formatMessage("error.cannot_have_mixed_length_replacement_vectors",
- new String[]{(mtch[i]), Integer.valueOf(idseq[i].length).toString(),Integer.valueOf(maxs).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.cannot_have_mixed_length_replacement_vectors",
+ new String[] { (mtch[i]),
+ Integer.valueOf(idseq[i].length).toString(),
+ Integer.valueOf(maxs).toString() }));
}
}
}
else
{
- throw new Error(MessageManager.getString("error.cannot_have_zero_length_vector_replacement_strings"));
+ throw new Error(
+ MessageManager
+ .getString("error.cannot_have_zero_length_vector_replacement_strings"));
}
}
// iterate through input, collating segments to be inserted into url
{
// just return the essential info about what the URL would be generated
// from
- return new Object[]
- { new int[]
- { seqsmatched }, thismatched };
+ return new Object[] { new int[] { seqsmatched }, thismatched };
}
// otherwise, create the URL completely.
}
}
- return new Object[]
- { new int[]
- { seqsmatched }, thismatched, matched, new String[]
- { submiturl.toString() } };
+ return new Object[] { new int[] { seqsmatched }, thismatched, matched,
+ new String[] { submiturl.toString() } };
}
/**
public static void main(String argv[])
{
// note - JAL-1383 - these services are all dead
- String[] links = new String[]
- {
+ String[] links = new String[] {
"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
*/
};
- SequenceI[] seqs = new SequenceI[]
- { new Sequence("StupidLabel:gi|9234|pdb|102L|A",
+ SequenceI[] seqs = new SequenceI[] { new Sequence(
+ "StupidLabel:gi|9234|pdb|102L|A",
"asdiasdpasdpadpwpadasdpaspdw"), };
String[][] seqsandids = formStrings(seqs);
for (int i = 0; i < links.length; i++)
}
-
public ImageMaker(Component parent, TYPE type, String title, int width,
int height, File file, String fileTitle)
{
{
setupPNG(width, height);
}
-
+
} catch (Exception ex)
{
- System.out.println("Error creating "
- + type.getName() + " file.");
+ System.out.println("Error creating " + type.getName() + " file.");
}
}
}
return graphics;
}
-
-
public void writeImage()
{
try
static JalviewFileChooser getPNGChooser()
{
if (Jalview.isHeadlessMode())
- {
+ {
return null;
}
return new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "png" }, new String[]
- { "Portable network graphics" }, "Portable network graphics");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "png" },
+ new String[] { "Portable network graphics" },
+ "Portable network graphics");
}
static JalviewFileChooser getEPSChooser()
return null;
}
return new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "eps" }, new String[]
- { "Encapsulated Postscript" }, "Encapsulated Postscript");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "eps" },
+ new String[] { "Encapsulated Postscript" },
+ "Encapsulated Postscript");
}
static JalviewFileChooser getSVGChooser()
{
if (Jalview.isHeadlessMode())
- {
+ {
return null;
}
return new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "svg" }, new String[]
- { "Scalable Vector Graphics" }, "Scalable Vector Graphics");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "svg" },
+ new String[] { "Scalable Vector Graphics" },
+ "Scalable Vector Graphics");
}
}
fromLowest = Math.min(fromLowest, from[i]);
fromHighest = Math.max(fromHighest, from[i + 1]);
- fromShifts.add(new int[]
- { from[i], from[i + 1] });
+ fromShifts.add(new int[] { from[i], from[i + 1] });
}
toLowest = to[0];
{
toLowest = Math.min(toLowest, to[i]);
toHighest = Math.max(toHighest, to[i + 1]);
- toShifts.add(new int[]
- { to[i], to[i + 1] });
+ toShifts.add(new int[] { to[i], to[i + 1] });
}
}
{
for (int[] r : map.fromShifts)
{
- fromShifts.add(new int[]
- { r[0], r[1] });
+ fromShifts.add(new int[] { r[0], r[1] });
}
}
if (map.toShifts != null)
{
for (int[] r : map.toShifts)
{
- toShifts.add(new int[]
- { r[0], r[1] });
+ toShifts.add(new int[] { r[0], r[1] });
}
}
}
* @param fromRatio
* @param toRatio
*/
- public MapList(List<int[]> fromRange, List<int[]> toRange,
- int fromRatio, int toRatio)
+ public MapList(List<int[]> fromRange, List<int[]> toRange, int fromRatio,
+ int toRatio)
{
this.fromShifts = fromRange;
this.toShifts = toRange;
fromLowest = Integer.MAX_VALUE;
fromHighest = 0;
- for (int[] range : fromRange) {
+ for (int[] range : fromRange)
+ {
fromLowest = Math.min(fromLowest, range[0]);
fromHighest = Math.max(fromHighest, range[1]);
}
* returning mapped position
*/
private int[][] posMap(List<int[]> shiftTo, int ratio,
- List<int[]> shiftFrom,
- int toRatio)
+ List<int[]> shiftFrom, int toRatio)
{
// TODO not used - remove??
int iv = 0, ivSize = shiftTo.size();
}
mp[i] = m;
}
- int[][] map = new int[][]
- { new int[]
- { from, to, tF, tT }, new int[to - from + 2] };
+ int[][] map = new int[][] { new int[] { from, to, tF, tT },
+ new int[to - from + 2] };
map[0][2] = tF;
map[0][3] = tT;
return null; // throw new Error("Bad Mapping!");
}
// System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
- return new int[]
- { toPos[0], fromRemainder, toPos[1] };
+ return new int[] { toPos[0], fromRemainder, toPos[1] };
}
/**
{
if (pos >= intv[0] && pos <= intv[1])
{
- return new int[]
- { count + pos - intv[0] + 1, +1 };
+ return new int[] { count + pos - intv[0] + 1, +1 };
}
else
{
{
if (pos >= intv[1] && pos <= intv[0])
{
- return new int[]
- { count + intv[0] - pos + 1, -1 };
+ return new int[] { count + intv[0] - pos + 1, -1 };
}
else
{
protected static int[] countToPos(List<int[]> shiftFrom, int pos)
{
int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
- int[] intv =
- { 0, 0 };
+ int[] intv = { 0, 0 };
while (iv < ivSize)
{
intv = shiftFrom.get(iv++);
{
if (pos <= count + 1 + diff)
{
- return new int[]
- { pos - count - 1 + intv[0], +1 };
+ return new int[] { pos - count - 1 + intv[0], +1 };
}
else
{
{
if (pos <= count + 1 - diff)
{
- return new int[]
- { intv[0] - (pos - count - 1), -1 };
+ return new int[] { intv[0] - (pos - count - 1), -1 };
}
else
{
* region to final position of ending region inclusive
*/
protected static int[] getIntervals(List<int[]> shiftFrom,
- int[] fromStart,
- int[] fromEnd, int fromRatio2)
+ int[] fromStart, int[] fromEnd, int fromRatio2)
{
if (fromStart == null || fromEnd == null)
{
i = fs;
// truncate initial interval
iv = shiftFrom.get(intv++);
- iv = new int[]
- { iv[0], iv[1] };// clone
+ iv = new int[] { iv[0], iv[1] };// clone
if (i == fs)
{
iv[0] = startpos;
{
ranges.add(iv); // add initial range
iv = shiftFrom.get(intv++); // get next interval
- iv = new int[]
- { iv[0], iv[1] };// clone
+ iv = new int[] { iv[0], iv[1] };// clone
i++;
}
if (i == fe)
i--;
}
iv = shiftFrom.get(i);
- iv = new int[]
- { iv[1], iv[0] };// reverse and clone
+ iv = new int[] { iv[1], iv[0] };// reverse and clone
// truncate initial interval
if (i == fs)
{
{ // fix apparent logic bug when fe==-1
ranges.add(iv); // add (truncated) reversed interval
iv = shiftFrom.get(i);
- iv = new int[]
- { iv[1], iv[0] }; // reverse and clone
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone
}
if (i == fe)
{
int[] mp = shiftTo(mpos);
if (mp != null)
{
- return new int[]
- { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
+ return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
}
return null;
}
int[] mp = shiftFrom(pos);
if (mp != null)
{
- return new int[]
- { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+ return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
}
return null;
}
package jalview.util;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
import jalview.commands.CommandI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
/**
* Helper methods for manipulations involving sequence mappings.
*
*/
int mappedEditPos = action == Action.DELETE_GAP ? match[0]
- mappedCount : match[0];
- Edit e = result.new Edit(action, new SequenceI[]
- { targetSeq }, mappedEditPos, mappedCount, gapChar);
+ Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
+ mappedEditPos, mappedCount, gapChar);
result.addEdit(e);
/*
*/
int startResiduePos = selected.findPosition(firstUngappedPos);
int endResiduePos = selected.findPosition(lastUngappedPos);
-
+
for (AlignedCodonFrame acf : codonFrames)
{
SequenceI mappedSequence = targetIsNucleotide ? acf
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq) : acf.getAaForDnaSeq(seq);
+ SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
+ : acf.getAaForDnaSeq(seq);
if (mappedSeq != null)
{
for (SequenceI seq2 : mapTo.getSequences())
{
return result;
}
- for (AlignedCodonFrame mapping : mappings) {
- if (mapping.involvesSequence(sequence)) {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(sequence))
+ {
result.add(mapping);
}
}
*/
public class ParseHtmlBodyAndLinks
{
- private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
String orig = null;
{
return Float.compare(values[o1], values[o2]);
}
-
+
}
static class IntComparator implements Comparator<Integer>
nextZeroValue++;
}
}
-
+
/*
* Copy zero values back to original arrays
*/
System.arraycopy(f1, 0, arr, 0, nextZeroValue);
System.arraycopy(s1, 0, s, 0, nextZeroValue);
-
+
if (nextZeroValue == arr.length)
{
return; // all zero
/*
* Sort the non-zero values
*/
- int[] nonZeroInts = Arrays
- .copyOfRange(f1, nextZeroValue, f1.length);
+ int[] nonZeroInts = Arrays.copyOfRange(f1, nextZeroValue, f1.length);
char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
externalSort(nonZeroInts, nonZeroChars);
// sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
-
+
/*
* Assemble sorted non-zero results
*/
{
this.iterator = stuff.listIterator(stuff.size());
}
+
@Override
public boolean hasNext()
{
}
if (sidx == shifts.size())
{
- shifts.add(sidx, new int[]
- { pos, shift });
+ shifts.add(sidx, new int[] { pos, shift });
}
else
{
{
if (sh != null)
{
- inverse.shifts.add(new int[]
- { sh[0], -sh[1] });
+ inverse.shifts.add(new int[] { sh[0], -sh[1] });
}
}
}
import java.util.List;
import java.util.regex.Pattern;
-
public class StringUtils
{
- private static final Pattern DELIMITERS_PATTERN = Pattern.compile(".*='[^']*(?!')");
+ private static final Pattern DELIMITERS_PATTERN = Pattern
+ .compile(".*='[^']*(?!')");
private static final boolean DEBUG = false;
* the character to insert
*/
public static final char[] insertCharAt(char[] in, int position,
- int count,
- char ch)
+ int count, char ch)
{
char[] tmp = new char[in.length + count];
-
+
if (position >= in.length)
{
System.arraycopy(in, 0, tmp, 0, in.length);
{
System.arraycopy(in, 0, tmp, 0, position);
}
-
+
int index = position;
while (count > 0)
{
tmp[index++] = ch;
count--;
}
-
+
if (position < in.length)
{
- System.arraycopy(in, position, tmp, index,
- in.length - position);
+ System.arraycopy(in, position, tmp, index, in.length - position);
}
-
+
return tmp;
}
*/
package jalview.util;
-import java.util.*;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import javax.swing.table.*;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumnModel;
+import javax.swing.table.TableModel;
/**
* TableSorter is a decorator for TableModels; adding sorting functionality to a
if (ns == 0)
{
// take whole regex
- return new String[]
- { rg.stringMatched(),
+ return new String[] { rg.stringMatched(),
url_prefix + rg.stringMatched() + url_suffix };
} /*
* else if (ns==1) { // take only subgroup match return new String[]
}
// just return simple url substitution.
- return new String[]
- { idstring, url_prefix + idstring + url_suffix };
+ return new String[] { idstring, url_prefix + idstring + url_suffix };
}
else
{
- return new String[]
- { "", url_prefix };
+ return new String[] { "", url_prefix };
}
}
public static void main(String argv[])
{
- String[] links = new String[]
- {
+ String[] links = new String[] {
/*
* "AlinkT|Target|http://foo.foo.soo/",
* "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
* , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
*/
"NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
- String[] idstrings = new String[]
- {
+ String[] idstrings = new String[] {
/*
* //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",
* //"123123312", "123123 ABCDE foo", "PFAM:PF23943",
return isDataset;
}
-
private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
protected ColumnSelection colSel = new ColumnSelection();
protected ColourSchemeI globalColourScheme = null;
-
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
*/
public boolean sortByTree = false;
-
/**
*
*
return alignment.getHiddenSequences().getSize() > 0;
}
-
protected SequenceGroup selectionGroup;
public void setSequenceSetId(String newid)
public void showSequence(int index)
{
List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
- index,
- hiddenRepSequences);
+ index, hiddenRepSequences);
if (tmp.size() > 0)
{
if (selectionGroup == null)
public boolean isHiddenRepSequence(SequenceI seq)
{
- return alignment.getSeqrep()==seq || (hiddenRepSequences != null
- && hiddenRepSequences.containsKey(seq));
+ return alignment.getSeqrep() == seq
+ || (hiddenRepSequences != null && hiddenRepSequences
+ .containsKey(seq));
}
public SequenceGroup getRepresentedSequences(SequenceI seq)
colSel.invertColumnSelection(0, alignment.getWidth());
}
-
@Override
public SequenceI[] getSelectionAsNewSequence()
{
return sequences;
}
-
@Override
public SequenceI[] getSequenceSelection()
{
return sequences;
}
-
@Override
- public CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
+ public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
return getAlignmentView(selectedOnly, false);
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
markGroups);
}
-
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
return selection;
}
-
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
}
}
- regions.add(new int[]
- { start, end });
+ regions.add(new int[] { start, end });
if (colSel != null && colSel.hasHiddenColumns())
{
}
@Override
- public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+ boolean selectedOnly)
{
ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
AlignmentAnnotation[] aa;
- if ((aa=alignment.getAlignmentAnnotation())!=null)
+ if ((aa = alignment.getAlignmentAnnotation()) != null)
{
- for (AlignmentAnnotation annot:aa)
+ for (AlignmentAnnotation annot : aa)
{
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
- if (selectedOnly && selectionGroup!=null)
+ if (selectedOnly && selectionGroup != null)
+ {
+ colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ selectionGroup.getEndRes(), clone);
+ }
+ else
{
- colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
- } else {
colSel.makeVisibleAnnotation(clone);
}
ala.add(clone);
return ala;
}
-
@Override
public boolean isPadGaps()
{
return padGaps;
}
-
@Override
public void setPadGaps(boolean padGaps)
{
}
oldrfs.clear();
}
+
@Override
public boolean isDisplayReferenceSeq()
{
@Override
public boolean areFeaturesDisplayed()
{
- return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+ return featuresDisplayed != null
+ && featuresDisplayed.getRegisterdFeaturesCount() > 0;
}
/**
{
viewStyle.setShowSequenceFeatures(b);
}
+
@Override
public boolean isShowSequenceFeatures()
{
return viewStyle.isShowSequenceFeaturesHeight();
}
-
-
@Override
public void setShowAnnotation(boolean b)
{
protected void broadcastCommand(CommandI command, boolean undo)
{
- getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+ getStructureSelectionManager().commandPerformed(command, undo,
+ getVamsasSource());
}
/**
return 0;
}
boolean iAmProtein = !getAlignment().isNucleotide();
- AlignmentI proteinAlignment = iAmProtein ? getAlignment()
- : complement.getAlignment();
+ AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
+ .getAlignment();
if (proteinAlignment == null)
{
return 0;
}
final Set<AlignedCodonFrame> mappings = proteinAlignment
.getCodonFrames();
-
+
/*
* Heuristic: find the first mapped sequence (if any) with a non-gapped
* residue in the middle column of the visible region. Scroll the
int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
final HiddenSequences hiddenSequences = getAlignment()
.getHiddenSequences();
-
+
/*
- * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+ * searching to the bottom of the alignment gives smoother scrolling across
+ * all gapped visible regions
*/
int lastSeq = alignment.getHeight() - 1;
for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
.findMappingsForSequence(sequence, mappings);
if (!seqMappings.isEmpty())
{
- break;
+ break;
}
}
-
+
if (sequence == null)
{
/*
*/
package jalview.viewmodel;
-import java.util.Vector;
-
import jalview.analysis.PCA;
+import jalview.api.RotatableCanvasI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
public class PCAModel
{
{
DISPLAY_STRING, DESCRIPTION;
}
+
private ThresholdType thresholdType;
private float thresholdValue;
}
if (!fdi.isRegistered(featureType))
{
- pushFeatureType(Arrays.asList(new String[]
- { featureType }));
+ pushFeatureType(Arrays.asList(new String[] { featureType }));
}
fdi.setVisible(featureType);
}
types.toArray(neworder);
if (renderOrder != null)
{
- System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+ System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
}
renderOrder = neworder;
protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
{
float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
- final byte[] r = new byte[]
- { 0, (byte) 255 };
+ final byte[] r = new byte[] { 0, (byte) 255 };
if (mm != null)
{
if (r[0] != 0 || mm[0] < 0.0)
float[][] mm = (float[][]) minmax.get(features[index].getType());
if (mm == null)
{
- mm = new float[][]
- { null, null };
+ mm = new float[][] { null, null };
minmax.put(features[index].getType(), mm);
}
if (mm[nonpos] == null)
{
- mm[nonpos] = new float[]
- { features[index].score, features[index].score };
+ mm[nonpos] = new float[] { features[index].score,
+ features[index].score };
}
else
{
if (initOrders)
{
- setOrder(oldRender[j], (1 - (1 + (float) j)
- / oldRender.length));
+ setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
}
if (allfeatures.contains(oldRender[j]))
{
{
if (renderOrder == null)
{
- return Arrays.asList(new String[]
- {});
+ return Arrays.asList(new String[] {});
}
return Arrays.asList(renderOrder);
}
float transparency, Hashtable featureOrder)
{
super();
- this.renderOrder = Arrays.copyOf(renderOrder,renderOrder.length);
+ this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
this.featureGroups = new ConcurrentHashMap(featureGroups);
this.featureColours = new ConcurrentHashMap(featureColours);
this.transparency = transparency;
package jalview.viewmodel.styles;
-import java.awt.Color;
-
import jalview.api.ViewStyleI;
+import java.awt.Color;
+
/**
* A container for holding alignment view properties. View properties are
* data-independent, which means they can be safely copied between views
&& getWrapAlignment() == vs.getWrapAlignment() && getWrappedWidth() == vs
.getWrappedWidth());
/*
- * and compare non-primitive types; syntax below will match null with null values
+ * and compare non-primitive types; syntax below will match null with null
+ * values
*/
match = match
&& String.valueOf(getFontName()).equals(
abovePIDThreshold = b;
}
-
/**
* DOCUMENT ME!
*
this.charWidth = w;
}
-
/**
* @param value
* indicating if subsequent colourscheme changes will be propagated
*/
package jalview.workers;
-import java.util.List;
-
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import java.util.List;
+
/**
* Base class for alignment calculation workers
*
package jalview.workers;
-import java.util.ConcurrentModificationException;
-import java.util.Hashtable;
-
import jalview.analysis.AAFrequency;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import java.util.ConcurrentModificationException;
+import java.util.Hashtable;
+
/**
* A thread to recompute the consensus of the cDNA complement for a linked
* protein alignment.
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.AAFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+import java.util.Hashtable;
+
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
SequenceI[] aseqs = getSequences();
- AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
- true);
+ AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
alignViewport.setSequenceConsensusHash(hconsensus);
setColourSchemeConsensus(hconsensus);
{
// Deal with Transaction exceptions
wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
- .formatMessage("info.server_exception", new Object[]
- { WebServiceName, ex.getMessage() }));
+ .formatMessage("info.server_exception", new Object[] {
+ WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
Cache.log
.debug("WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
+ wsInfo.appendProgressText(MessageManager
+ .getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
{
if (dbSources == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ sequence.getDBRef(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[]
- { dbSource });
+ entry.getDBRef(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[]
- { sequence.getStart() + absStart,
+ mp = new Mapping(null, new int[] {
+ sequence.getStart() + absStart,
sequence.getStart() + absStart + entrySeq.length() - 1 },
- new int[]
- { entry.getStart(),
+ new int[] { entry.getStart(),
entry.getStart() + entrySeq.length() - 1 }, 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end
reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
- MessageManager.getString("label.find_uniprot_accession_ids"),
+ MessageManager
+ .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager
+ .getString("label.find_uniprot_accession_ids"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
}
startTime = System.currentTimeMillis();
if (af != null)
{
- af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.fetching_das_sequence_features"),
+ startTime);
}
if (sourceRegistry == null)
{
source));
for (String id : idl)
{
- List<String> qid = Arrays.asList(new String[]
- { id });
+ List<String> qid = Arrays.asList(new String[] { id });
try
{
DasGFFAdapter dga = featuresc.fetchData(source, qid);
if (af != null)
{
- af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
+ af.setProgressBar(
+ MessageManager.getString("status.no_das_sources_active"),
+ startTime);
}
if (getFeatSettings() != null)
{
{
if (af != null)
{
- af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.das_feature_fetching_cancelled"),
+ startTime);
}
cancelled = true;
}
if (!cancelled && af != null)
{
// only update the progress bar if we've completed the fetch normally
- af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.das_feature_fetching_complete"), startTime);
}
if (af != null && af.featureSettings != null)
return null;
}
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- {
+ seq.getDBRef(), new String[] {
// jalview.datamodel.DBRefSource.PDB,
jalview.datamodel.DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
}
}
- return new Object[]
- { ids, qstring };
+ return new Object[] { ids, qstring };
}
/**
*/
public static BufferedReader doHttpUrlPost(String postUrl,
List<NameValuePair> vals, int connectionTimeoutMs,
- int readTimeoutMs) throws ClientProtocolException,
- IOException
+ int readTimeoutMs) throws ClientProtocolException, IOException
{
// todo use HttpClient 4.3 or later and class RequestConfig
HttpParams params = new BasicHttpParams();
*/
package jalview.ws;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
/**
* This is the the concrete implementation of the sequence retrieval interface
* and abstract class in jalview.ws.seqfetcher. This implements the run-time
{
nm = nm.substring(4);
}
- dassrc.add(new String[]
- { srcs[i], nm.toUpperCase() });
+ dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
}
else
{
- nondas.add(new String[]
- { srcs[i], nm.toUpperCase() });
+ nondas.add(new String[] { srcs[i], nm.toUpperCase() });
}
}
}
}
else
{
- noProds.addElement((dna ? new Object[]
- { al, al } : new Object[]
- { al }));
+ noProds.addElement((dna ? new Object[] { al, al }
+ : new Object[] { al }));
}
}
}
if (ds == null)
{
- ds = new Alignment(new SequenceI[]
- { sq });
+ ds = new Alignment(new SequenceI[] { sq });
}
else
*/
package jalview.ws;
-import jalview.gui.*;
+import jalview.gui.WebserviceInfo;
public abstract class WSClient // implements WSMenuEntryProviderI
{
*/
package jalview.ws.dbsources;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl
{
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
{
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
/**
* @author JimP
*
*/
package jalview.ws.dbsources;
-import java.io.File;
-
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import java.io.File;
+
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
} catch (Exception e)
{
stopQuery();
- throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
+ throw new Exception(MessageManager.formatMessage(
+ "exception.ebiembl_retrieval_failed_on", new String[] {
+ emprefx.toLowerCase(), query.trim() }), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
}
else
{
- result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
+ result.append(MessageManager.formatMessage(
+ "label.no_embl_record_found",
+ new String[] { emprefx.toLowerCase(), query.trim() }));
}
}
if (efile != null)
if (seqs != null && seqs.length > 0)
{
al = new Alignment(seqs);
- result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
+ result.append(MessageManager.formatMessage(
+ "label.embl_successfully_parsed", new String[] { emprefx }));
results = result;
}
stopQuery();
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
/**
* Test class for accessing GeneDB - not yet finished.
*
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
-
/**
* A rest client for querying the Search endpoing of the PDB REST API
*
for (SequenceI pdbcs : toremove)
{
pdbfile.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation()!=null)
+ if (pdbcs.getAnnotation() != null)
{
- for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
{
pdbfile.deleteAnnotation(aa);
}
if (pdbfile == null || pdbfile.getHeight() < 1)
{
- throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.no_pdb_records_for_chain", new String[] { id,
+ ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
* to an alignment TODO: create interface to pass alignment properties and tree
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
/**
* Contains methods for fetching sequences from Rfam database
*
name.append(n);
}
- if (entry.getProtein() != null
- && entry.getProtein().getName() != null)
+ if (entry.getProtein() != null && entry.getProtein().getName() != null)
{
for (String nm : entry.getProtein().getName())
{
*/
package jalview.ws.dbsources.das.api;
-import java.util.List;
-
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.util.List;
+
import org.biodas.jdas.schema.sources.MAINTAINER;
import org.biodas.jdas.schema.sources.VERSION;
*/
package jalview.ws.dbsources.das.datamodel;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import com.stevesoft.pat.Regex;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.*;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
/**
* an instance of this class is created for each unique DAS Sequence source (ie
* one capable of handling the 'sequence' for a particular MapMaster)
if (!(jsrc = new JalviewSource(source, connprops, false))
.isSequenceSource())
{
- throw new Exception(MessageManager.formatMessage("exception.das_source_doesnt_support_sequence_command", new String[]{source.getTitle()}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.das_source_doesnt_support_sequence_command",
+ new String[] { source.getTitle() }));
}
this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
this.source = source;
connprops.getConnectionPropertyProviderFor(sr));
for (String q : toks)
{
- List<String> qset = Arrays.asList(new String[]
- { q });
+ List<String> qset = Arrays.asList(new String[] { q });
try
{
DasSequenceAdapter s = sq.fetchData(sr, qset);
*/
package jalview.ws.dbsources.das.datamodel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Date;
import org.biodas.jdas.schema.sources.SOURCE;
import org.biodas.jdas.schema.sources.VERSION;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
public class JalviewSource implements jalviewSourceI
{
SOURCE source;
int p = cap.getQueryUri().lastIndexOf(capname);
if (p < -1)
{
- throw new Exception(MessageManager.formatMessage("exception.invalid_das_source", new String[]{source.getUri()}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.invalid_das_source",
+ new String[] { source.getUri() }));
}
if (cap.getQueryUri().charAt(p) == '/')
{
*/
package jalview.ws.ebi;
+import jalview.util.MessageManager;
+
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
import java.util.List;
import java.util.StringTokenizer;
-import jalview.util.MessageManager;
-
/**
* DOCUMENT ME!
*
* pair list {String,JvDataType} giving a mime-type followed by its associated
* JvDataType enumeration.
*/
- final public static Object[] typemap = new Object[]
- { "application/x-align", JvDataType.ALIGNMENT,
+ final public static Object[] typemap = new Object[] {
+ "application/x-align", JvDataType.ALIGNMENT,
"application/x-jalview-annotation", JvDataType.ANNOTATION,
"application/x-newick", JvDataType.TREE,
"application/x-new-hampshire", JvDataType.TREE,
*/
package jalview.ws.jws1;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
}
else
{
- throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+ throw new IOException(
+ MessageManager
+ .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}
jalview.bin.Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices =
- {
+ ServiceHandle[] defServices = {
new ServiceHandle(
"MsaWS",
"Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")),
+ MessageManager
+ .getString("label.muscle_multiple_protein_sequence_alignment")),
new ServiceHandle(
"MsaWS",
"Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ " Nucleic Acids Research, 33 511-518",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- MessageManager.getString("label.mafft_multiple_sequence_alignment")),
+ MessageManager
+ .getString("label.mafft_multiple_sequence_alignment")),
new ServiceHandle(
"MsaWS",
"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ " Nucleic Acids Research, 22 4673-4680",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- MessageManager.getString("label.clustalw_multiple_sequence_alignment")),
+ MessageManager
+ .getString("label.clustalw_multiple_sequence_alignment")),
new ServiceHandle(
"SecStrPred",
"Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
{
if (jalview.gui.Desktop.desktop != null)
{
- JOptionPane
- .showMessageDialog(
- jalview.gui.Desktop.desktop,
- MessageManager.getString("label.set_proxy_settings"),
- MessageManager.getString("label.proxy_authorization_failed"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.set_proxy_settings"),
+ MessageManager
+ .getString("label.proxy_authorization_failed"),
+ JOptionPane.WARNING_MESSAGE);
}
}
else
{
if (!msa && msf.length > 1)
{
- throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
}
String altitle = getPredictionName(WebServiceName) + " for "
private WebserviceInfo setWebService()
{
WebServiceName = "JNetWS";
- WebServiceJobTitle = MessageManager.getString("label.jnet_secondary_structure_prediction");
+ WebServiceJobTitle = MessageManager
+ .getString("label.jnet_secondary_structure_prediction");
WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+ "Proteins 40:502-511\".";
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
- MessageManager.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
- wsInfo.setProgressText(MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL})
- + "\n"
- + ex.getMessage());
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .formatMessage(
+ "label.secondary_structure_prediction_service_couldnt_be_located",
+ new String[] { WebServiceName, WsURL }),
+ MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
+ wsInfo.setProgressText(MessageManager
+ .formatMessage(
+ "label.secondary_structure_prediction_service_couldnt_be_located",
+ new String[] { WebServiceName, WsURL })
+ + "\n" + ex.getMessage());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
{
sqs[i] = al.getSequenceAt(i);
}
- if (!jalview.analysis.SeqsetUtils.deuniquify(
- SequenceInfo, sqs))
+ if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
{
- throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
+ throw (new Exception(
+ MessageManager
+ .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
}
else
{
- throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.unknown_format_for_file", new String[] {
+ format, result.getAligfile() })));
}
}
else
.getAlignmentAndColumnSelection(gc)[0];
if (this.msaIndex >= sqs.length)
{
- throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// Uses RemoveGapsCommand
// ///
- new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
- new SequenceI[]
- { sqs[msaIndex] }, currentView);
+ new jalview.commands.RemoveGapsCommand(
+ MessageManager.getString("label.remove_gaps"),
+ new SequenceI[] { sqs[msaIndex] }, currentView);
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), SequenceInfo))
{
- throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
+ throw (new Exception(
+ MessageManager
+ .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
}
else
{
alant.sequenceRef);
}
}
- return new Object[]
- { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
}
/**
if (job.hasValidInput())
{
OutputHeader = wsInfo.getProgressText();
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
job.setJobnum(0);
}
else
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
if (job.hasValidInput())
{
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
OutputHeader = wsInfo.getProgressText();
job.setJobnum(0);
}
{
if (!(j instanceof JPredJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_startjob_called",
+ new String[] { j.getClass().toString() }));
}
try
{
{
job.result = new JpredResult();
job.result.setInvalid(true);
- job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
+ job.result.setStatus(MessageManager.formatMessage(
+ "label.submission_params", new String[] { job.getJobId()
+ .toString() }));
throw new Exception(job.getJobId());
}
else
}
else
{
- throw new Exception(MessageManager.getString("exception.server_timeout_try_later"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
{
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
// JBPNote - this could be a popup informing the user of the problem.
- wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()}));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .formatMessage(
+ "info.failed_to_submit_prediction",
+ new String[] { e.getMessage(),
+ wsInfo.getProgressText() }));
jalview.bin.Cache.log.debug(
"Failed Submission of job " + j.getJobnum(), e);
else
{
// do merge with other job results
- throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented"));
+ throw new Error(
+ MessageManager
+ .getString("error.multiple_jnet_subjob_merge_not_implemented"));
}
} catch (Exception e)
{
"JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), e.getMessage() }));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .formatMessage("info.invalid_jnet_job_result_data",
+ new String[] { OutputHeader.toString(),
+ j.result.getStatus(), e.getMessage() }));
j.result.setBroken(true);
}
}
*/
package jalview.ws.jws1;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
import jalview.ws.AWSThread;
/**
*/
package jalview.ws.jws1;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.MuscleWS;
+import ext.vamsas.MuscleWSServiceLocator;
+import ext.vamsas.MuscleWSSoapBindingStub;
+import ext.vamsas.ServiceHandle;
/**
* DOCUMENT ME!
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.getName()}),
- MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.service_called_is_not_msa_service",
+ new String[] { sh.getName() }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
- JOptionPane.showMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.getName()}),
- MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.msa_service_is_unknown",
+ new String[] { sh.getName() }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
class MsaWSThread extends JWS1Thread implements WSClientI
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
this.seqs = new vamsas.objects.simple.SequenceSet();
jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- { alseqs, msaorder };
+ return new Object[] { alseqs, msaorder };
}
return null;
}
{
if (!(job instanceof MsaWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+ j.result.setStatus(MessageManager
+ .getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
if (jobsubmit == null)
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.appendProgressText(
- j.getJobnum(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
.getMsa();
if (valign != null)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(),
- MessageManager.getString("info.alignment_object_method_notes"));
+ wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+ .getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
*/
package jalview.ws.jws1;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.SeqSearchI;
+import ext.vamsas.SeqSearchServiceLocator;
+import ext.vamsas.SeqSearchServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
/**
* DOCUMENT ME!
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.service_called_is_not_seq_search_service", new String[]{sh.getName()}),
- MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage(
+ "label.service_called_is_not_seq_search_service",
+ new String[] { sh.getName() }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.seq_search_service_is_unknown", new String[]{sh.getName()}),
- MessageManager.getString("label.internal_jalview_error"),
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.seq_search_service_is_unknown",
+ new String[] { sh.getName() }), MessageManager
+ .getString("label.internal_jalview_error"),
JOptionPane.WARNING_MESSAGE);
return;
}
if (!locateWebService())
{
- throw new Exception(MessageManager.formatMessage("exception.cannot_contact_service_endpoint_at", new String[]{WsURL}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.cannot_contact_service_endpoint_at",
+ new String[] { WsURL }));
}
String database = server.getDatabase();
if (database == null)
{
- dbParamsForEndpoint.put(WsURL, new String[]
- {});
+ dbParamsForEndpoint.put(WsURL, new String[] {});
return null;
}
StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
import jalview.io.NewickFile;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
import vamsas.objects.simple.SeqSearchResult;
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
if (submitGaps)
* trigger a 'fetchDBids' to annotate sequences with database ids...
*/
- return new Object[]
- { al, nf };
+ return new Object[] { al, nf };
}
return null;
}
{
if (!(job instanceof SeqSearchWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+ j.result.setStatus(MessageManager
+ .getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
if (jobsubmit == null)
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.appendProgressText(
- j.getJobnum(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
.getAlignment();
if (valign != null)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(),
- MessageManager.getString("info.alignment_object_method_notes"));
+ wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+ .getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{this.alTitle}));
+ af.ShowNewickTree(nf, MessageManager.formatMessage(
+ "label.tree_from", new String[] { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
{
if (serviceHandle == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_attach_ws_menu_entry"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_attach_ws_menu_entry"));
}
attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
}
Map<String, String[]> fmap;
featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("Glob", new String[]
- { "Globular Domain", "Predicted globular domain" });
+ fmap.put("Glob", new String[] { "Globular Domain",
+ "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
fmap = new HashMap<String, String[]>());
featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("REM465", new String[]
- { "REM465", "Missing density" });
- fmap.put("HOTLOOPS", new String[]
- { "HOTLOOPS", "Flexible loops" });
- fmap.put("COILS", new String[]
- { "COILS", "Random coil" });
+ fmap.put("REM465", new String[] { "REM465", "Missing density" });
+ fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
+ fmap.put("COILS", new String[] { "COILS", "Random coil" });
featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("GlobDoms", new String[]
- { "Globular Domain", "Predicted globular domain" });
- fmap.put("Disorder", new String[]
- { "Protein Disorder", "Probable unstructured peptide region" });
+ fmap.put("GlobDoms", new String[] { "Globular Domain",
+ "Predicted globular domain" });
+ fmap.put("Disorder", new String[] { "Protein Disorder",
+ "Probable unstructured peptide region" });
Map<String, Map<String, Object>> amap;
annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("Dydx", new HashMap<String, Object>());
amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
- amap.get("Dydx").put(THRESHOLD, new double[]
- { 1, 0 });
- amap.get("Dydx").put(RANGE, new float[]
- { -1, +1 });
+ amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
+ amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
amap.put("SmoothedScore", new HashMap<String, Object>());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.put("COILS", new HashMap<String, Object>());
amap.put("HOTLOOPS", new HashMap<String, Object>());
amap.put("REM465", new HashMap<String, Object>());
- amap.get("COILS").put(THRESHOLD, new double[]
- { 1, 0.516 });
- amap.get("COILS").put(RANGE, new float[]
- { 0, 1 });
-
- amap.get("HOTLOOPS").put(THRESHOLD, new double[]
- { 1, 0.6 });
- amap.get("HOTLOOPS").put(RANGE, new float[]
- { 0, 1 });
- amap.get("REM465").put(THRESHOLD, new double[]
- { 1, 0.1204 });
- amap.get("REM465").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
+ amap.get("COILS").put(RANGE, new float[] { 0, 1 });
+
+ amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
+ amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
+ amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
+ amap.get("REM465").put(RANGE, new float[] { 0, 1 });
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("Long", new HashMap<String, Object>());
amap.put("Short", new HashMap<String, Object>());
- amap.get("Long").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("Long").put(RANGE, new float[]
- { 0, 1 });
- amap.get("Short").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("Short").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Long").put(RANGE, new float[] { 0, 1 });
+ amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Short").put(RANGE, new float[] { 0, 1 });
annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("JRonn", new HashMap<String, Object>());
- amap.get("JRonn").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("JRonn").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
@Override
if (type == null)
{
// create a default type for this feature
- type = new String[]
- { typeName + " (" + scr.getMethod() + ")",
+ type = new String[] {
+ typeName + " (" + scr.getMethod() + ")",
service.getActionText() };
}
if (vals.hasNext())
typename = service.serviceType + " ("
+ scr.getMethod() + ")",
calcName = service.getServiceTypeURI() + "/"
- + scr.getMethod(),
- aseq, base + 1, scr);
+ + scr.getMethod(), aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
Map<String, Object> styleMap = (annotTypeMap == null) ? null
/**
* validate input for dynamic/non-dynamic update context
+ *
* @param dynamic
* @param seqs
* @return true if input is valid
*/
- abstract boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs);
+ abstract boolean checkValidInputSeqs(boolean dynamic,
+ List<FastaSequence> seqs);
abstract String submitToService(
List<compbio.data.sequence.FastaSequence> seqs)
String id = rslt;
if (cancelJob(rslt))
{
- System.err.println("Cancelled job "+id);
+ System.err.println("Cancelled job " + id);
}
- else
+ else
{
- System.err.println("Job "+id+" couldn't be cancelled.");
+ System.err.println("Job " + id + " couldn't be cancelled.");
}
} catch (Exception q)
{
String[] k = jpredRowLabels.get(fsq.getId());
if (k == null)
{
- k = new String[]
- { fsq.getId(), "JNet Output" };
+ k = new String[] { fsq.getId(), "JNet Output" };
}
if (fsq.getId().startsWith("JNETSOL"))
{
{
sol[spos] = '0';
}
- if (vseq[spos] == 'B' && (sol[spos]=='0' || sol[spos] < amnt))
+ if (vseq[spos] == 'B'
+ && (sol[spos] == '0' || sol[spos] < amnt))
{
sol[spos] = amnt;
}
try
{
elm[i] = new Annotation("" + annot, "" + annot, annot,
- Integer.valueOf(""+annot));
+ Integer.valueOf("" + annot));
} catch (Exception x)
{
System.err.println("Expected numeric value in character '"
*/
package jalview.ws.jws2;
-import compbio.metadata.JobStatus;
-
import jalview.ws.AWsJob;
+import compbio.metadata.JobStatus;
+
/**
* job status processing for JWS2 jobs.
*
*/
package jalview.ws.jws2;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.dm.JabaParameter;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.dm.JabaOption;
-import jalview.ws.jws2.dm.JabaParameter;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.params.WsParamSetI;
-
public class JabaParamStore implements ParamDatastoreI
{
}
if (narg == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_handle_jaba_param",
+ new String[] { rg.getClass().toString() }));
}
else
{
.getOption() : null;
if (narg == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_handle_jaba_param",
+ new String[] { rg.getClass().toString() }));
}
else
{
}
if (servicePresets.containsKey(name))
{
- throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_attempt_to_delete_service_preset"));
}
}
List<ArgumentI> jobParams)
{
JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
- jps.setApplicableUrls(new String[]
- { service.getUri() });
+ jps.setApplicableUrls(new String[] { service.getUri() });
editedParams.put(jps.getName(), jps);
if (manager != null)
{
: getPreset(presetName));
if (jps == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_cannot_locate_oldname_presetname",
+ new String[] { oldName, presetName }));
}
jps.setName(presetName);
jps.setDescription(text);
jps.setArguments(jobParams);
- jps.setApplicableUrls(new String[]
- { service.getUri() });
+ jps.setApplicableUrls(new String[] { service.getUri() });
if (oldName != null && !oldName.equals(jps.getName()))
{
editedParams.remove(oldName);
{
if (!involves(urls))
{
- throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set"));
+ throw new IOException(
+ MessageManager
+ .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
}
JabaWsParamSet wsp = new JabaWsParamSet();
{
if (!involves(pset.getApplicableUrls()))
{
- throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{service.getUri()}));
+ throw new IOException(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
+ new String[] { service.getUri() }));
}
if (!(pset instanceof JabaWsParamSet))
{
- throw new Error(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
}
StringBuffer rslt = new StringBuffer();
@Override
public String[] getApplicableUrls()
{
- return new String[]
- { service.getUri() };
+ return new String[] { service.getUri() };
}
@Override
@Override
public void setSourceFile(String newfile)
{
- throw new Error(MessageManager.formatMessage("error.cannot_set_source_file_for", new String[]{getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.cannot_set_source_file_for", new String[] { getClass()
+ .toString() }));
}
@Override
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(MessageManager.getString("error.mismatch_service_instance_preset"));
+ throw new Error(
+ MessageManager
+ .getString("error.mismatch_service_instance_preset"));
}
}
@Override
public void setArguments(List<ArgumentI> args)
{
- throw new Error(MessageManager.getString("error.cannot_set_params_for_ws_preset"));
+ throw new Error(
+ MessageManager
+ .getString("error.cannot_set_params_for_ws_preset"));
}
}
this.jwsserver = server;
}
- Services[] JABAWS1SERVERS = new Services[]
- { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
- Services.ProbconsWS, Services.TcoffeeWS };
+ Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
+ Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+ Services.TcoffeeWS };
- Services[] JABAWS2SERVERS = new Services[]
- { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
- Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
- Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
- Services.JronnWS, Services.RNAalifoldWS };
+ Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
+ Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+ Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
+ Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
+ Services.RNAalifoldWS };
/*
* (non-Javadoc)
service = Jws2Client.connect(jwsserver, srv);
} catch (Exception e)
{
- System.err.println("Jws2 Discoverer: Problem on "
- + jwsserver + " with service " + srv + ":\n"
- + e.getMessage());
+ System.err.println("Jws2 Discoverer: Problem on " + jwsserver
+ + " with service " + srv + ":\n" + e.getMessage());
if (!(e instanceof javax.xml.ws.WebServiceException))
{
e.printStackTrace();
{
// return Jws2Client.validURL(jwsserver); // checks syntax only
boolean result = false;
- if (server != null) {
- try {
+ if (server != null)
+ {
+ try
+ {
URL url = new URL(server);
url.openStream().close();
result = true;
rslt = aaservice.customAnalize(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+ throw new JobSubmissionException(
+ MessageManager
+ .getString("exception.jobsubmission_invalid_params_set"),
+ x);
}
}
*/
package jalview.ws.jws2;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
import java.util.Iterator;
import java.util.List;
import compbio.data.msa.MsaWS;
-import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker extends
+ AbstractJabaCalcWorker
{
@SuppressWarnings("unchecked")
super(alignViewport, alignPanel);
}
- public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
+ AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
rslt = msaservice.customAlign(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+ throw new JobSubmissionException(
+ MessageManager
+ .getString("exception.jobsubmission_invalid_params_set"),
+ x);
}
}
return rslt;
* arguments. for (Argument opt : arguments) { newargs.add(opt); } }
* paramset = newargs; } else {
*/
- throw new Error(MessageManager.getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
}
}
else
*/
abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame);
-
protected boolean registerAAConWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
aaui.getAAconToggle());
- aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
+ aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aaui.getAAconToggleTooltip()));
aaConEnabled.addActionListener(new ActionListener()
{
@Override
});
wsmenu.add(aaConEnabled);
final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(false, aaui.getAAeditSettingsTooltip()
- + "</p>") + "</html>");
+ modifyParams
+ .setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(false,
+ aaui.getAAeditSettingsTooltip() + "</p>")
+ + "</html>");
modifyParams.addActionListener(new ActionListener()
{
{
// TODO raise dialog box explaining error, and/or open the JABA
// preferences menu.
- throw new Error(MessageManager.getString("error.no_aacon_service_found"));
+ throw new Error(
+ MessageManager.getString("error.no_aacon_service_found"));
}
return new AAConSettings(true, service, null, null);
}
this.aborted = aborted;
}
+
public void run()
{
// first set up exclusion list if needed
final Set<String> ignoredServices = new HashSet<String>();
- for (String ignored : Cache.getDefault(
- "IGNORED_JABAWS_SERVICETYPES", "")
- .split("\\|"))
+ for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
+ "").split("\\|"))
{
ignoredServices.add(ignored);
}
service.attachWSMenuEntry(atpoint, alignFrame);
if (alternates.containsKey(service.serviceType))
{
- atpoint.add(hitm = new JMenu(MessageManager.getString("label.switch_server")));
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip(false, MessageManager.getString("label.choose_jabaws_server")));
+ atpoint.add(hitm = new JMenu(MessageManager
+ .getString("label.switch_server")));
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+ MessageManager.getString("label.choose_jabaws_server")));
for (final Jws2Instance sv : alternates.get(service.serviceType))
{
JMenuItem itm;
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText(MessageManager.formatMessage("label.services_at", new String[]{host}));
+ atpoint.setToolTipText(MessageManager.formatMessage(
+ "label.services_at", new String[] { host }));
}
}
if (bytype)
Desktop.showUrl(service.getHost());
}
});
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip(true, MessageManager.getString("label.open_jabaws_web_page")));
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_jabaws_web_page")));
lasthostFor.put(service.action, host);
}
hostLabels.add(host + service.serviceType
}
} catch (MalformedURLException ex)
{
- Cache.log
- .warn("Problem whilst trying to make a URL from '"
- + ((url != null) ? url : "<null>") + "'");
+ Cache.log.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
Cache.log
.warn("This was probably due to a malformed comma separated list"
+ " in the "
}
} catch (Exception ex)
{
- Cache.log.warn(
- "Error parsing comma separated list of urls in "
- + JWS2HOSTURLS + " preference.", ex);
+ Cache.log.warn("Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
}
return urls;
}
{
try
{
- compbio.ws.client.WSTester.main(new String[]
- { "-h=" + foo.toString() });
+ compbio.ws.client.WSTester
+ .main(new String[] { "-h=" + foo.toString() });
} catch (Exception e)
{
e.printStackTrace();
// redundant at mo - but may change
JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.service_called_is_not_msa_service",
- new String[]
- { sh.serviceType }), MessageManager
+ new String[] { sh.serviceType }), MessageManager
.getString("label.internal_jalview_error"),
JOptionPane.WARNING_MESSAGE);
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.msa_service_is_unknown", new String[]
- { sh.serviceType }), MessageManager
+ .formatMessage("label.msa_service_is_unknown",
+ new String[] { sh.serviceType }), MessageManager
.getString("label.internal_jalview_error"),
JOptionPane.WARNING_MESSAGE);
startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
-
}
public MsaWSClient()
System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
}
-
-
protected String getServiceActionKey()
{
return "MsaWS";
{
action = "Realign ";
msawsmenu = new JMenu(MessageManager.formatMessage(
- "label.realign_with_params", new String[]
- { svcname }));
+ "label.realign_with_params", new String[] { svcname }));
msawsmenu.setToolTipText(MessageManager
.getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
final boolean withGaps = submitGaps;
JMenuItem method = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings", new String[]
- { calcName }));
- method.setToolTipText(MessageManager.formatMessage(
- "label.action_with_default_settings", new String[]
- { action }));
+ "label.calcname_with_default_settings",
+ new String[] { calcName }));
+ method.setToolTipText(MessageManager
+ .formatMessage("label.action_with_default_settings",
+ new String[] { action }));
method.addActionListener(new ActionListener()
{
if (msa != null)
{
- new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
- true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+ true, alignFrame.getViewport().getAlignment()
+ .getDataset(), alignFrame);
}
}
if (msa != null)
{
new MsaWSClient(service, null, null, true, alignFrame
- .getTitle(), msa, withGaps, true, alignFrame
- .getViewport().getAlignment().getDataset(), alignFrame);
+ .getTitle(), msa, withGaps, true, alignFrame
+ .getViewport().getAlignment().getDataset(),
+ alignFrame);
}
}
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(MessageManager.formatMessage(
- "label.run_with_preset_params", new String[]
- { calcName }));
+ JMenu presetlist = new JMenu(
+ MessageManager.formatMessage(
+ "label.run_with_preset_params",
+ new String[] { calcName }));
final int showToolTipFor = ToolTipManager.sharedInstance()
.getDismissDelay();
@Override
public void mouseExited(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+ ToolTipManager.sharedInstance().setDismissDelay(
+ showToolTipFor);
}
});
if (msa != null)
{
MsaWSClient msac = new MsaWSClient(service, preset,
- alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ alignFrame.getTitle(), msa, false, true,
+ alignFrame.getViewport().getAlignment()
+ .getDataset(), alignFrame);
}
}
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
return valid;
jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- { alseqs, msaorder };
+ return new Object[] { alseqs, msaorder };
}
return null;
}
{
return validInput;
}
+
public boolean isCancellable()
{
return true;
// boiler plate template
if (!(job instanceof MsaWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
}
else
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_server_doesnt_support_program",
+ new String[] { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (compbio.metadata.LimitExceededException _lex)
{
lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_exceeded_hard_limit",
+ new String[] { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (compbio.metadata.WrongParameterException _lex)
{
lex = _lex;
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_incorrect_param_setting",
+ new String[] { _lex.getMessage() }));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
// TODO: JBPNote catch timeout or other fault types explicitly
j.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(j.getJobnum(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
}
}
}
public void parseResult()
{
long progbar = System.currentTimeMillis();
- wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"),
+ progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
* SplitFrame with the other pane similarly aligned.
*/
AlignFrame requestedBy = getRequestingAlignFrame();
- if (requestedBy != null && requestedBy.getSplitViewContainer() != null
- && requestedBy.getSplitViewContainer().getComplement(requestedBy)!=null)
+ if (requestedBy != null
+ && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer().getComplement(
+ requestedBy) != null)
{
AlignmentI complement = requestedBy.getSplitViewContainer()
.getComplement(requestedBy);
import jalview.util.MessageManager;
-import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
-import compbio.metadata.*;
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.RunnerConfig;
+import compbio.metadata.ValueConstrain;
+import compbio.metadata.WrongParameterException;
public class ParameterUtils
{
}
else
{
- copy.addOptionNames(names.toArray(new String[]
- {}));
+ copy.addOptionNames(names.toArray(new String[] {}));
}
}
try
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(MessageManager.getString("error.implementation_error_couldnt_copy_value_constraint"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_couldnt_copy_value_constraint"));
}
}
List<String> pv = parameter.getPossibleValues();
if (pv != null)
{
- copy.addPossibleValues(pv.toArray(new String[]
- {}));
+ copy.addPossibleValues(pv.toArray(new String[] {}));
}
setOptionFrom(copy, parameter);
return copy;
description = typename;
}
- return new String[]
- { typename, description };
+ return new String[] { typename, description };
}
// Check whether, at position i there is a base contact and return all the
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import java.awt.event.ActionListener;
import java.util.List;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
/**
* @author jprocter
try
{
worker = (AbstractJabaCalcWorker) (clientClass
- .getConstructor(new Class[]
- { Jws2Instance.class, AlignFrame.class,
- WsParamSetI.class, List.class })
- .newInstance(new Object[]
- { sh, alignFrame, this.preset, paramset }));
+ .getConstructor(new Class[] { Jws2Instance.class,
+ AlignFrame.class, WsParamSetI.class, List.class })
+ .newInstance(new Object[] { sh, alignFrame, this.preset,
+ paramset }));
} catch (Exception x)
{
x.printStackTrace();
- throw new Error(MessageManager.getString("error.implementation_error"), x);
+ throw new Error(
+ MessageManager.getString("error.implementation_error"), x);
}
alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
service.serviceType.length() - 2);
JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings", new String[]
- { calcName }));
+ "label.calcname_with_default_settings",
+ new String[] { calcName }));
annotservice.addActionListener(new ActionListener()
{
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset", new String[]{calcName}));
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset", new String[] { calcName }));
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
- + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
- : MessageManager.getString("label.service_preset")) + "</strong><br/>"
- + preset.getDescription()));
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ "<strong>"
+ + (preset.isModifiable() ? MessageManager
+ .getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
Desktop.instance.showUrl(service.docUrl);
}
});
- annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.view_service_doc_url", new String[]{service.docUrl,service.docUrl})));
+ annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("label.view_service_doc_url",
+ new String[] { service.docUrl, service.docUrl })));
wsmenu.add(annotservice);
}
}
*/
package jalview.ws.jws2.dm;
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-
import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Argument;
+import compbio.metadata.Option;
+
/**
* preferences for running AACon service
*
return;
}
// Try even harder to migrate arguments.
- throw new Error(MessageManager.getString("error.parameter_migration_not_implemented_yet"));
+ throw new Error(
+ MessageManager
+ .getString("error.parameter_migration_not_implemented_yet"));
}
}
@Override
public String[] getServiceURLs()
{
- return new String[]
- { service.getUri() };
+ return new String[] { service.getUri() };
}
}
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(MessageManager.getString("error.implementation_error_cannot_set_jaba_option"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_set_jaba_option"));
}
}
import jalview.ws.jws2.ParameterUtils;
import jalview.ws.params.ParameterI;
import jalview.ws.params.ValueConstrainI;
+
import compbio.metadata.Parameter;
import compbio.metadata.ValueConstrain;
*/
package jalview.ws.jws2.dm;
-import compbio.metadata.ValueConstrain;
-
import jalview.util.MessageManager;
import jalview.ws.params.ValueConstrainI;
+import compbio.metadata.ValueConstrain;
+
public class JabaValueConstrain implements ValueConstrainI
{
{
return ValueType.Integer;
}
- throw new Error(MessageManager.formatMessage("error.implementation_error_valuetype_doesnt_support_jabaws_type", new String[]{vc.toString()}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_valuetype_doesnt_support_jabaws_type",
+ new String[] { vc.toString() }));
}
@Override
*/
package jalview.ws.jws2.dm;
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Option;
-
import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Option;
+
public class JabaWsParamSet implements WsParamSetI
{
/**
{
if (!allJaba(jobParams))
{
- throw new Error(MessageManager.getString("error.cannot_create_jabaws_param_set"));
+ throw new Error(
+ MessageManager
+ .getString("error.cannot_create_jabaws_param_set"));
}
else
{
{
if (!allJaba(args))
{
- throw new Error(MessageManager.getString("error.cannot_set_arguments_to_jabaws_param_set"));
+ throw new Error(
+ MessageManager
+ .getString("error.cannot_set_arguments_to_jabaws_param_set"));
}
jabaArguments = new ArrayList<Option>();
for (ArgumentI rg : args)
{
return ((SequenceAnnotation) service).getRunnerOptions();
}
- throw new Error(MessageManager.formatMessage("error.implementation_error_runner_config_not_available", new String[]{serviceType,service.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_runner_config_not_available",
+ new String[] { serviceType, service.getClass().toString() }));
}
@Override
private static HashMap<String, AlignAnalysisUIText> aaConGUI;
private static HashSet<String> ignoreGUI;
+
private static String category_rewrite(String cat_name)
{
return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
init();
return (ignoreGUI.contains(serviceType.toString()));
}
+
/**
* construct a service instance and configure it with any additional
* properties needed so Jalview can access it correctly
*/
package jalview.ws.params.simple;
+import jalview.ws.params.OptionI;
+
import java.net.URL;
import java.util.Arrays;
-import jalview.ws.params.OptionI;
-
public class BooleanOption extends Option implements OptionI
{
{
super(name, descr, required, (defVal ? name : ""), (val ? name : ""),
- Arrays.asList(new String[]
- { name }), link);
+ Arrays.asList(new String[] { name }), link);
}
}
import jalview.bin.Cache;
import jalview.io.FileParse;
import jalview.io.packed.DataProvider;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.io.packed.ParsePackedSet;
import jalview.io.packed.SimpleDataProvider;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.io.mime.JalviewMimeContentHandler;
if (en == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_need_to_have_httpresponse"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_need_to_have_httpresponse"));
}
jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
// Decide how we deal with content.
*/
public abstract class InputType
{
- private static final Pattern URL_PATTERN = Pattern.compile("^([^=]+)=?'?([^']*)?'?");
+ private static final Pattern URL_PATTERN = Pattern
+ .compile("^([^=]+)=?'?([^']*)?'?");
/**
* not used yet
*/
package jalview.ws.rest;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
/**
* @author JimP
*
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage("label.webservice_job_title", new String[]{service.details.Action,service.details.Name});
+ WebServiceJobTitle = MessageManager.formatMessage(
+ "label.webservice_job_title", new String[] {
+ service.details.Action, service.details.Name });
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(MessageManager.formatMessage("label.rest_client_submit", new String[]{service.details.Action,service.details.Name}));
+ submit.setToolTipText(MessageManager.formatMessage(
+ "label.rest_client_submit", new String[] {
+ service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
else
{
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), false, true);
}
- viewTitle = MessageManager.formatMessage("label.select_unselect_visible_regions_from", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_unselect_visible_regions_from",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
else
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
}
else
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), null, av.hasHiddenColumns(), false,
true);
- viewTitle = "" + (av.hasHiddenColumns() ? (new StringBuffer(" ").append(MessageManager.getString("label.visible_region_of")).toString()) : "")
- + af.getTitle();
+ viewTitle = ""
+ + (av.hasHiddenColumns() ? (new StringBuffer(" ")
+ .append(MessageManager
+ .getString("label.visible_region_of"))
+ .toString()) : "") + af.getTitle();
}
RestJobThread jobsthread = new RestJobThread(this);
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : MessageManager.getString("label.job_couldnt_be_started_check_input")),
- MessageManager.getString("label.unable_start_web_service_analysis"),
+ : MessageManager
+ .getString("label.job_couldnt_be_started_check_input")),
+ MessageManager
+ .getString("label.unable_start_web_service_analysis"),
JOptionPane.WARNING_MESSAGE);
}
}
public static RestClient makeShmmrRestClient()
{
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager.getString("label.multiharmony");
+ String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
+ .getString("label.multiharmony");
Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
jalview.ws.rest.params.JobConstant toolp;
// toolp = new jalview.ws.rest.JobConstant("tool","jalview");
*/
package jalview.ws.rest;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Hashtable;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.SeqGroupIndexVector;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
public class RestJob extends AWsJob
{
jobs = new RestJob[viscontigals.length];
for (int j = 0; j < jobs.length; j++)
{
- int[] visc = new int[]
- { viscontig[j * 2], viscontig[j * 2 + 1] };
+ int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] };
if (j != 0)
{
jobs[j] = new RestJob(j, this, viscontigals[j], visc);
destAls.add(destAl);
destColsel.add(destCs);
resultDest.add(AddDataTo.newAlignment);
- throw new Error(MessageManager.getString("error.implementation_error")+"TODO: ");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error")
+ + "TODO: ");
}
}
/**
{
AlignmentI destal;
ColumnSelection destcs;
- String alTitle = MessageManager.formatMessage("label.webservice_job_title_on", new String[]{restClient.service.details.Action,restClient.service.details.Name,restClient.viewTitle});
+ String alTitle = MessageManager.formatMessage(
+ "label.webservice_job_title_on", new String[] {
+ restClient.service.details.Action,
+ restClient.service.details.Name, restClient.viewTitle });
switch (action)
{
case newAlignment:
*/
package jalview.ws.rest;
+import jalview.datamodel.SequenceI;
+import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.StringUtils;
+import jalview.ws.rest.params.Alignment;
+import jalview.ws.rest.params.AnnotationFile;
+import jalview.ws.rest.params.SeqGroupIndexVector;
+
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider.JvDataType;
-import jalview.util.StringUtils;
-import jalview.ws.rest.params.Alignment;
-import jalview.ws.rest.params.AnnotationFile;
-import jalview.ws.rest.params.SeqGroupIndexVector;
-
public class RestServiceDescription
{
- private static final Pattern PARAM_ENCODED_URL_PATTERN = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$");
+ private static final Pattern PARAM_ENCODED_URL_PATTERN = Pattern
+ .compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$");
/**
* create a new rest service description ready to be configured
;
vls.add(new String("gapCharacter='" + gapCharacter + "'"));
vls.add(new String("returns='" + _genOutputFormatString() + "'"));
- return StringUtils.arrayToSeparatorList(vls.toArray(new String[0]), ",");
+ return StringUtils
+ .arrayToSeparatorList(vls.toArray(new String[0]), ",");
}
public String toString()
url.append("$");
url.append(param.getValue().getURLtokenPrefix());
url.append(":");
- url.append(StringUtils.arrayToSeparatorList(vals.toArray(new String[0]),
- ","));
+ url.append(StringUtils.arrayToSeparatorList(
+ vals.toArray(new String[0]), ","));
url.append("$");
}
}
boolean valid = true;
int lastp = 0;
String url = new String();
- Matcher prms = PARAM_ENCODED_URL_PATTERN
- .matcher(ipurl);
+ Matcher prms = PARAM_ENCODED_URL_PATTERN.matcher(ipurl);
Map<String, InputType> iparams = new Hashtable<String, InputType>();
InputType jinput;
while (prms.find())
public static Class[] getInputTypes()
{
// TODO - find a better way of maintaining this classlist
- return new Class[]
- { jalview.ws.rest.params.Alignment.class,
+ return new Class[] { jalview.ws.rest.params.Alignment.class,
jalview.ws.rest.params.AnnotationFile.class,
SeqGroupIndexVector.class,
jalview.ws.rest.params.SeqIdVector.class,
if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
{
ArrayList<String> al = new ArrayList<String>();
- for (String prprm : StringUtils.separatorListToArray(iprmparams, ","))
+ for (String prprm : StringUtils.separatorListToArray(iprmparams,
+ ","))
{
// hack to ensure that strings like "sep=','" containing unescaped
// commas as values are concatenated
{
public Alignment()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
String format = "FASTA";
{
public AnnotationFile()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
if (tok.startsWith("format"))
{
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
if (val.equalsIgnoreCase(fmt))
{
}
warnings.append("Invalid annotation file format '" + val
+ "'. Must be one of (");
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
warnings.append(" " + fmt);
}
// TODO - consider disregarding base options here.
List<OptionI> lst = getBaseOptions();
lst.add(new Option("format", "Alignment annotation upload format",
- true, JVANNOT, format, Arrays.asList(new String[]
- { JVANNOT, CSVANNOT }), null));
+ true, JVANNOT, format, Arrays.asList(new String[] { JVANNOT,
+ CSVANNOT }), null));
return lst;
}
}
prm.add(URLEncoder.encode(value, "UTF-8"));
} catch (UnsupportedEncodingException ex)
{
- throw new Error(MessageManager.formatMessage("error.couldnt_encode_as_utf8", new String[]{value}), ex);
+ throw new Error(MessageManager.formatMessage(
+ "error.couldnt_encode_as_utf8", new String[] { value }), ex);
}
}
{
public SeqGroupIndexVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException(MessageManager.formatMessage("exception.notvaliddata_group_contains_less_than_min_seqs", new String[]{Integer.valueOf(minsize).toString()}));
+ throw new NoValidInputDataException(
+ MessageManager
+ .formatMessage(
+ "exception.notvaliddata_group_contains_less_than_min_seqs",
+ new String[] { Integer.valueOf(minsize)
+ .toString() }));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
}
if (se == null)
{
- se = new int[]
- { p, p };
+ se = new int[] { p, p };
}
else
{
{
if (lowest - 1 > minsize)
{
- gl.add(0, new int[]
- { 0, lowest - 2 });
+ gl.add(0, new int[] { 0, lowest - 2 });
}
if ((al.getHeight() - 1 - highest) > minsize)
{
- gl.add(new int[]
- { highest + 1, al.getHeight() - 1 });
+ gl.add(new int[] { highest + 1, al.getHeight() - 1 });
}
}
else
{
- gl.add(new int[]
- { 0, al.getHeight() - 1 });
+ gl.add(new int[] { 0, al.getHeight() - 1 });
}
if (min >= 0 && gl.size() < min)
{
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[]
- { " ", ",", ";", "\t", "|" }), null));
+ sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ null));
lst.add(new IntegerParameter("minsize",
"Minimum size of partition allowed by service", true, 1,
minsize, 1, 0));
{
public SeqIdVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[]
- { " ", ",", ";", "\t", "|" }), null));
+ sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
return lst;
}
public SeqVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
@Override
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[]
- { " ", ",", ";", "\t", "|" }), null));
+ sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ null));
lst.add(createMolTypeOption("type", "Sequence type", false, type,
molType.MIX));
{
public Tree()
{
- super(new Class[]
- { jalview.analysis.NJTree.class });
+ super(new Class[] { jalview.analysis.NJTree.class });
}
// TODO specify modifiers for tree output format
/*
* rj.getTreeForInput(token); return new StringBody(new )
*/
- throw new Error(MessageManager.getString("error.tree_inputtype_not_yet_implemented"));
+ throw new Error(
+ MessageManager
+ .getString("error.tree_inputtype_not_yet_implemented"));
// return null;
}
*/
package jalview.ws.seqfetcher;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Stack;
import java.util.Vector;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-
public class ASequenceFetcher
{
} catch (Exception e)
{
// Serious problems if this happens.
- throw new Error(MessageManager.getString("error.dbrefsource_implementation_exception"), e);
+ throw new Error(
+ MessageManager
+ .getString("error.dbrefsource_implementation_exception"),
+ e);
}
addDbRefSourceImpl(proxy);
}
{
if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_dbinstance_must_implement_interface", new String[]{class1.toString()}));
+ throw new Error(
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_dbinstance_must_implement_interface",
+ new String[] { class1.toString() }));
}
if (FETCHABLEDBS == null)
{
*/
package jalview.ws.uimodel;
-import java.util.HashMap;
public class AlignAnalysisUIText
{
package jalview.ws.uimodel;
-
import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
this.searchSummary = searchSummary;
}
-
/**
* Convenience method to obtain a Table model for a given summary List based
* on the request parameters
if (request.getAssociatedSequence() != null)
{
tableModel.addColumn("Ref Sequence"); // Create sequence column header if
- // exists in the request
+ // exists in the request
}
for (PDBDocField field : request.getWantedFields())
{
for (PDBDocField field : diplayFields)
{
String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
- : pdbJsonDoc
- .get(field.getCode()).toString();
+ : pdbJsonDoc.get(field.getCode()).toString();
if (field.equals(PDBDocField.PDB_ID))
{
this.pdbId = fieldData;
}
}
-
import jalview.util.MessageManager;
-import java.io.*;
-import java.util.*;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.StringWriter;
+import java.io.Writer;
+import java.util.Date;
/**
* This represents an EPS document. Several EpsGraphics2D objects may point to
_bufferedWriter.write(line + "\n");
} catch (IOException e)
{
- throw new EpsException(MessageManager.formatMessage("exception.eps_coudnt_write_output_file", new String[]{e.getMessage()}));
+ throw new EpsException(MessageManager.formatMessage(
+ "exception.eps_coudnt_write_output_file",
+ new String[] { e.getMessage() }));
}
}
import jalview.util.MessageManager;
-import java.io.*;
-import java.text.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.font.*;
-import java.awt.geom.*;
-import java.awt.image.*;
-import java.awt.image.renderable.*;
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Composite;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.GraphicsConfiguration;
+import java.awt.GraphicsDevice;
+import java.awt.GraphicsEnvironment;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.Polygon;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.font.FontRenderContext;
+import java.awt.font.GlyphVector;
+import java.awt.font.TextAttribute;
+import java.awt.font.TextLayout;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Arc2D;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.geom.RoundRectangle2D;
+import java.awt.image.BufferedImage;
+import java.awt.image.BufferedImageOp;
+import java.awt.image.ColorModel;
+import java.awt.image.ImageObserver;
+import java.awt.image.PixelGrabber;
+import java.awt.image.RenderedImage;
+import java.awt.image.WritableRaster;
+import java.awt.image.renderable.RenderableImage;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.StringWriter;
+import java.text.AttributedCharacterIterator;
+import java.text.AttributedString;
+import java.text.CharacterIterator;
+import java.util.Hashtable;
+import java.util.Map;
/**
* EpsGraphics2D is suitable for creating high quality EPS graphics for use in
*/
private void methodNotSupported()
{
- EpsException e = new EpsException(MessageManager.formatMessage("exception.eps_method_not_supported", new String[]{VERSION}));
+ EpsException e = new EpsException(MessageManager.formatMessage(
+ "exception.eps_method_not_supported", new String[] { VERSION }));
e.printStackTrace(System.err);
}
ColorModel cm = img.getColorModel();
WritableRaster wr = img.copyData(null);
- BufferedImage img1 = new BufferedImage(cm, wr, cm
- .isAlphaPremultiplied(), properties);
+ BufferedImage img1 = new BufferedImage(cm, wr,
+ cm.isAlphaPremultiplied(), properties);
AffineTransform at = AffineTransform.getTranslateInstance(
img.getMinX(), img.getMinY());
at.preConcatenate(xform);
return t.createTransformedShape(_clip);
} catch (Exception e)
{
- throw new EpsException(MessageManager.formatMessage("exception.eps_unable_to_get_inverse_matrix", new String[]{_transform.toString()}));
+ throw new EpsException(MessageManager.formatMessage(
+ "exception.eps_unable_to_get_inverse_matrix",
+ new String[] { _transform.toString() }));
}
}
}
matrix = matrix.createInverse();
} catch (Exception e)
{
- throw new EpsException(MessageManager.formatMessage("exception.eps_unable_to_get_inverse_matrix", new String[]{matrix.toString()}));
+ throw new EpsException(MessageManager.formatMessage(
+ "exception.eps_unable_to_get_inverse_matrix",
+ new String[] { matrix.toString() }));
}
matrix.scale(1, -1);
matrix.getMatrix(m);
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "poll"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobid, type });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
+ type });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "runWUBlast"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { params, content });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { params,
+ content });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "test"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobid, type });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
+ type });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "checkStatus"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobid });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "getResults"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobid });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "polljob"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { jobid, outformat });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
+ outformat });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "doWUBlast"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { params, content });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { params,
+ content });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call
- .invoke(new java.lang.Object[]
- { sequence, searchDatabases, taxonId,
- new java.lang.Boolean(onlyActive) });
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
+ sequence, searchDatabases, taxonId,
+ new java.lang.Boolean(onlyActive) });
if (_resp instanceof java.rmi.RemoteException)
{
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- { accession, ac_version, searchDatabases, taxonId,
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
+ accession, ac_version, searchDatabases, taxonId,
new java.lang.Boolean(onlyActive) });
if (_resp instanceof java.rmi.RemoteException)
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[]
- {});
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
if (_resp instanceof java.rmi.RemoteException)
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.no_stub_implementation_for_interface",
+ new String[] { (serviceEndpointInterface == null ? "null"
+ : serviceEndpointInterface.getName()) }));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+ throw new javax.xml.rpc.ServiceException(
+ MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[] { portName }));
}
}
*/
package vamsas;
-import vamsas.objects.simple.*;
+import vamsas.objects.simple.Alignment;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SequenceSet;
+import vamsas.objects.simple.WsJobId;
public interface IMsaWS
{