<xs:attribute name="colour" type="xs:int" />
</xs:complexType>
</xs:element>
+ <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="name" type="xs:string" />
+ <xs:attribute name="value" type="xs:string" />
+ </xs:complexType>
+ </xs:element>
</xs:sequence>
<xs:attribute name="graph" type="xs:boolean" use="required" />
<xs:attribute name="graphType" type="xs:int" use="optional" />
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
public int offset;
- public Sequence sequence;
+ /**
+ * sequence is the sequence extracted by the chain parsing code
+ */
+ public SequenceI sequence;
+
+ /**
+ * shadow is the sequence created by any other parsing processes (e.g. Jmol,
+ * RNAview)
+ */
+ public SequenceI shadow = null;
public boolean isNa = false;
*/
protected String newline = System.getProperty("line.separator");
+ public Mapping shadowMap;
+
public void setNewlineString(String nl)
{
newline = nl;
public void transferResidueAnnotation(StructureMapping mapping)
{
SequenceI sq = mapping.getSequence();
+ SequenceI dsq = sq;
if (sq != null)
{
- if (sequence != null && sequence.getAnnotation() != null)
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ // any annotation will be transferred onto the dataset sequence
+
+ if (shadow != null && shadow.getAnnotation() != null)
{
+ for (AlignmentAnnotation ana : shadow.getAnnotation())
+ {
+ List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana.liftOver(sequence, shadowMap);
+ mapping.transfer(ana);
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ else
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ana : sequence.getAnnotation())
+ {
+ List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ mapping.transfer(ana);
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
}
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class PDBfile extends jalview.io.AlignFile
{
- public Vector chains;
+ public Vector<PDBChain> chains;
public String id;
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ SequenceI dataset = chains.elementAt(i).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- if (((PDBChain) chains.elementAt(i)).id != null)
+ if (chains.elementAt(i).id != null)
{
entry.getProperty().put("CHAIN",
- ((PDBChain) chains.elementAt(i)).id);
+ chains.elementAt(i).id);
}
if (inFile != null)
{
markCalcIds();
}
- private static String calcIdPrefix = "JalviewPDB:";
+ private static String calcIdPrefix = "JalviewPDB";
public static boolean isCalcIdHandled(String calcId)
{
return calcId != null
- && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
- calcIdPrefix,
- calcIdPrefix.length() + 1) > -1);
+ && (calcIdPrefix.equals(calcId));
}
- public static boolean isCalcIdForFile(String calcId, String pdbFile)
+
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan, String pdbFile)
{
- return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
- + ":" + calcIdPrefix));
+ return alan.getCalcId() != null
+ && calcIdPrefix.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
public static String relocateCalcId(String calcId,
{
oldId = "";
}
- aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+ aa.setCalcId(calcIdPrefix);
+ aa.setProperty("PDBID", id);
+ aa.setProperty("oldCalcId", oldId);
}
}
}
sq.getPDBId().clear();
}
}
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
}
} catch (ClassNotFoundException q)
{
}
}
+ private void replaceAndUpdateChains(ArrayList<SequenceI> prot,
+ AlignmentI al, String pep, boolean b)
+ {
+ List<List<? extends Object>> replaced = AlignSeq
+ .replaceMatchingSeqsWith(seqs,
+ annotations, prot, al, AlignSeq.PEP, false);
+ for (PDBChain ch : chains)
+ {
+ int p = 0;
+ for (SequenceI sq : (List<SequenceI>) replaced.get(0))
+ {
+ p++;
+ if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
+ {
+ p = -p;
+ break;
+ }
+ }
+ if (p < 0)
+ {
+ p = -p - 1;
+ // set shadow entry for chains
+ ch.shadow = (SequenceI) replaced.get(1).get(p);
+ ch.shadowMap = ((AlignSeq) replaced.get(2)
+.get(p))
+ .getMappingFromS1(false);
+ }
+ }
+ }
+
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
throws Exception
{
{
if (sq.getDatasetSequence() != null)
{
- sq.getDatasetSequence().getPDBId().clear();
+ if (sq.getDatasetSequence().getPDBId() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
}
else
{
- sq.getPDBId().clear();
+ if (sq.getPDBId() != null)
+ {
+ sq.getPDBId().clear();
+ }
}
}
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
}
} catch (ClassNotFoundException x)
{
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeResidueList();
+ chains.elementAt(i).makeResidueList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ chains.elementAt(i).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ if (chains.elementAt(i).id.equals(id))
{
- return (PDBChain) chains.elementAt(i);
+ return chains.elementAt(i);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChargeColours();
+ chains.elementAt(i).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ chains.elementAt(i).setChainColours(cs);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ chains.elementAt(i).setChainColours(Color.getHSBColor(
1.0f / i, .4f, 1.0f));
}
}
* @param ochains
* @param al
* @param dnaOrProtein
- * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
+ * @param removeOldAnnots
+ * when true, old annotation is cleared before new annotation
+ * transferred
+ * @return List<List<SequenceI> originals, List<SequenceI> replacement,
+ * List<AlignSeq> alignment between each>
*/
- public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
+ public static List<List<? extends Object>> replaceMatchingSeqsWith(
+ List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
+ 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>();
if (al != null && al.getHeight() > 0)
{
ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
if ((q = ochains.indexOf(sp)) > -1)
{
seqs.set(p, sq = matches.get(q));
+ orig.add(sp);
+ repl.add(sq);
sq.setName(sp.getName());
sq.setDescription(sp.getDescription());
Mapping sp2sq;
sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+ aligs.add(aligns.get(q));
int inspos = -1;
for (int ap = 0; ap < annotations.size();)
{
}
}
}
+ return Arrays.asList(orig, repl, aligs);
}
/**
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
+ {
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
else
{
if (features == null)
+ {
features = "";
+ }
}
return features;
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
.size()]);
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
return true;
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.historyList.removeElement(command);
ap.alignFrame.updateEditMenuBar();
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
}
ap.paintAlignment(true);
{
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
+ {
seqs = new SequenceI[]
{ matcher == null ? (Sequence) newAlignFrame
.getAlignViewport().getAlignment()
.findName(sequence) : matcher.findIdMatch(sequence) };
+ }
}
else
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager.getStructureSelectionManager(
+ applet).registerPDBEntry(pdb);
}
else
{
// note separator local variable intentionally masks object field
int seplen = separator.length();
if (list == null || list.equals("") || list.equals(separator))
+ {
return null;
+ }
java.util.Vector jv = new Vector();
int cp = 0, pos;
while ((pos = list.indexOf(separator, cp)) > cp)
*/
package jalview.commands;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.Hashtable;
+import java.util.List;
/**
*
@Override
final public void undoCommand(AlignmentI[] views)
- {
- int e = 0, eSize = edits.length;
- for (e = eSize - 1; e > -1; e--)
- {
- switch (edits[e].command)
- {
- case INSERT_GAP:
- deleteGap(edits[e]);
- break;
- case DELETE_GAP:
- insertGap(edits[e]);
- break;
- case CUT:
- paste(edits[e], views);
- break;
- case PASTE:
- cut(edits[e], views);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
- }
+ {
+ for(Edit e : edits){
+ switch (e.command)
+ {
+ case INSERT_GAP:
+ deleteGap(e);
+ break;
+ case DELETE_GAP:
+ insertGap(e);
+ break;
+ case CUT:
+ paste(e, views);
+ break;
+ case PASTE:
+ cut(e, views);
+ break;
+ case REPLACE:
+ replace(e);
+ break;
+ }
}
}
List<SequenceI> sequences;
synchronized (sequences = command.al.getSequences())
{
- sequences.add(command.alIndex[i], command.seqs[i]);
+ if (!(command.alIndex[i] < 0))
+ {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
}
}
else
+ command.number);
}
if (command.seqs[i].getStart() == start)
+ {
newstart--;
+ }
else
+ {
newend++;
+ }
}
}
command.string[i] = null;
{
temp = new Annotation[aSize + command.number];
if (annotations[a].padGaps)
+ {
for (int aa = 0; aa < temp.length; aa++)
{
temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
}
+ }
}
else
{
int copylen = Math.min(command.position,
annotations[a].annotations.length);
if (copylen > 0)
+ {
System.arraycopy(annotations[a].annotations, 0, temp, 0,
copylen); // command.position);
+ }
Annotation[] deleted = new Annotation[command.number];
if (copylen >= command.position)
import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Map.Entry;
/**
*/
public boolean autoCalculated = false;
+ /**
+ * unique ID for this annotation, used to match up the same annotation row
+ * shown in multiple views and alignments
+ */
public String annotationId;
+ /**
+ * the sequence this annotation is associated with (or null)
+ */
public SequenceI sequenceRef;
- /** DOCUMENT ME!! */
+ /** label shown in dropdown menus and in the annotation label area */
public String label;
- /** DOCUMENT ME!! */
+ /** longer description text shown as a tooltip */
public String description;
- /** DOCUMENT ME!! */
+ /** Array of annotations placed in the current coordinate system */
public Annotation[] annotations;
public ArrayList<SimpleBP> bps = null;
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
+ /**
+ * map of positions in the associated annotation
+ */
public java.util.Hashtable<Integer, Annotation> sequenceMapping;
/** DOCUMENT ME!! */
this.scaleColLabel = annotation.scaleColLabel;
this.showAllColLabels = annotation.showAllColLabels;
this.calcId = annotation.calcId;
+ if (annotation.properties!=null)
+ {
+ properties = new HashMap<String,String>();
+ for (Map.Entry<String, String> val:annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
{
threshold = new GraphLine(annotation.threshold);
}
+ Annotation[] ann = annotation.annotations;
if (annotation.annotations != null)
{
- Annotation[] ann = annotation.annotations;
this.annotations = new Annotation[ann.length];
for (int i = 0; i < ann.length; i++)
{
}
}
}
- ;
- if (annotation.sequenceRef != null)
+ }
+ if (annotation.sequenceRef != null)
+ {
+ this.sequenceRef = annotation.sequenceRef;
+ if (annotation.sequenceMapping != null)
{
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
+ Integer p = null;
+ sequenceMapping = new Hashtable();
+ Enumeration pos = annotation.sequenceMapping.keys();
+ while (pos.hasMoreElements())
{
- Integer p = null;
- sequenceMapping = new Hashtable();
- Enumeration pos = annotation.sequenceMapping.keys();
- while (pos.hasMoreElements())
+ // could optimise this!
+ p = (Integer) pos.nextElement();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
{
- // could optimise this!
- p = (Integer) pos.nextElement();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
for (int i = 0; i < ann.length; i++)
{
if (ann[i] == a)
}
}
}
- else
- {
- this.sequenceMapping = null;
- }
+ }
+ else
+ {
+ this.sequenceMapping = null;
}
}
// TODO: check if we need to do this: JAL-952
protected String calcId = "";
/**
+ * properties associated with the calcId
+ */
+ protected Map<String, String> properties = new HashMap<String, String>();
+
+ /**
* base colour for line graphs. If null, will be set automatically by
* searching the alignment annotation
*/
// trim positions
}
}
+ }
+
+ /**
+ * like liftOver but more general.
+ *
+ * Takes an array of int pairs that will be used to update the internal
+ * sequenceMapping and so shuffle the annotated positions
+ *
+ * @param newref
+ * - new sequence reference for the annotation row - if null,
+ * sequenceRef is left unchanged
+ * @param mapping
+ * array of ints containing corresponding positions
+ * @param from
+ * - column for current coordinate system (-1 for index+1)
+ * @param to
+ * - column for destination coordinate system (-1 for index+1)
+ * @param idxoffset
+ * - offset added to index when referencing either coordinate system
+ * @note no checks are made as to whether from and/or to are sensible
+ * @note caller should add the remapped annotation to newref if they have not
+ * already
+ */
+ public void remap(SequenceI newref, int[][] mapping, int from, int to,
+ int idxoffset)
+ {
+ if (mapping != null)
+ {
+ Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+ int index = -1;
+ for (int mp[] : mapping)
+ {
+ if (index++ < 0)
+ {
+ continue;
+ }
+ Annotation ann = null;
+ if (from == -1)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
+ }
+ else
+ {
+ if (mp != null && mp.length > from)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(mp[from]));
+ }
+ }
+ if (ann != null)
+ {
+ if (to == -1)
+ {
+ remap.put(Integer.valueOf(idxoffset + index), ann);
+ }
+ else
+ {
+ if (to > -1 && to < mp.length)
+ {
+ remap.put(Integer.valueOf(mp[to]), ann);
+ }
+ }
+ }
+ }
+ sequenceMapping = remap;
+ old.clear();
+ if (newref != null)
+ {
+ sequenceRef = newref;
+ }
+ adjustForAlignment();
+ }
+ }
+
+ public String getProperty(String property)
+ {
+ if (properties == null)
+ {
+ return null;
+ }
+ return properties.get(property);
+ }
+ public void setProperty(String property, String value)
+ {
+ if (properties==null)
+ {
+ properties = new HashMap<String,String>();
+ }
+ properties.put(property, value);
+ }
+
+ public boolean hasProperties()
+ {
+ return properties != null && properties.size() > 0;
+ }
+
+ public Collection<String> getProperties()
+ {
+ if (properties == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+ return properties.keySet();
}
}
*/
package jalview.ext.jmol;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+import jalview.util.MessageManager;
+
import java.io.IOException;
import java.util.Hashtable;
import java.util.Map;
import org.jmol.viewer.Viewer;
import org.openscience.jmol.app.JmolApp;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.io.AlignFile;
-import jalview.io.FileParse;
-import jalview.util.MessageManager;
-
/**
* Import and process PDB files with Jmol
*
case MEASURE:
String mystatus = (String) data[3];
if (mystatus.indexOf("Picked") >= 0
- || mystatus.indexOf("Sequence") >= 0) // picking mode
+ || mystatus.indexOf("Sequence") >= 0)
+ {
+ // Picking mode
sendConsoleMessage(strInfo);
+ }
else if (mystatus.indexOf("Completed") >= 0)
+ {
sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
strInfo.length() - 1));
+ }
break;
case MESSAGE:
sendConsoleMessage(data == null ? null : strInfo);
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(currentAnnotation.label))
+ if (aa.label.equals(currentAnnotation.label)
+ && (currentAnnotation.getCalcId() == null ? aa.getCalcId() == null
+ : currentAnnotation.getCalcId()
+ .equals(aa.getCalcId())))
{
- aa.threshold.value = thr;
+ if (aa.threshold == null)
+ {
+ aa.threshold = new GraphLine(currentAnnotation.threshold);
+ }
+ else
+ {
+ aa.threshold.value = thr;
+ }
}
}
}
*/
package jalview.gui;
-import javax.swing.JOptionPane;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+
/**
* GUI related routines for associating PDB files with sequences
*
* @param sequence
*/
public PDBEntry associatePdbWithSeq(String choice, String protocol,
- SequenceI sequence, boolean prompt)
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
MCview.PDBfile pdbfile = null;
- try
+ pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, choice, protocol);
+ if (pdbfile == null)
{
- // TODO JAL-674 extract secondary structure and transfer it to associated
- // sequence
- pdbfile = new MCview.PDBfile(false, false, choice, protocol);
- if (pdbfile.id == null)
- {
- String reply = null;
-
- if (prompt)
- {
- reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager
- .getString("label.couldnt_find_pdb_id_in_file"),
- MessageManager.getString("label.no_pdb_id_in_file"),
- JOptionPane.QUESTION_MESSAGE);
- }
- if (reply == null)
- {
- return null;
- }
+ // stacktrace already thrown so just return
+ return null;
+ }
+ if (pdbfile.id == null)
+ {
+ String reply = null;
- entry.setId(reply);
+ if (prompt)
+ {
+ reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JOptionPane.QUESTION_MESSAGE);
}
- else
+ if (reply == null)
{
- entry.setId(pdbfile.id);
+ return null;
}
- } catch (java.io.IOException ex)
+ entry.setId(reply);
+ }
+ else
{
- ex.printStackTrace();
+ entry.setId(pdbfile.id);
}
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ if (pdbfile != null)
+ {
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .registerPDBEntry(entry);
+ }
return entry;
}
}
*/
package jalview.gui;
-import java.awt.Rectangle;
-import java.io.*;
-import java.lang.reflect.InvocationTargetException;
-import java.net.*;
-import java.util.*;
-import java.util.Map.Entry;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.schemabinding.version2.*;
-import jalview.schemes.*;
+import jalview.schemabinding.version2.AlcodMap;
+import jalview.schemabinding.version2.Alcodon;
+import jalview.schemabinding.version2.AlcodonFrame;
+import jalview.schemabinding.version2.Annotation;
+import jalview.schemabinding.version2.AnnotationColours;
+import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.CalcIdParam;
+import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.Features;
+import jalview.schemabinding.version2.Group;
+import jalview.schemabinding.version2.HiddenColumns;
+import jalview.schemabinding.version2.JGroup;
+import jalview.schemabinding.version2.JSeq;
+import jalview.schemabinding.version2.JalviewModel;
+import jalview.schemabinding.version2.JalviewModelSequence;
+import jalview.schemabinding.version2.MapListFrom;
+import jalview.schemabinding.version2.MapListTo;
+import jalview.schemabinding.version2.Mapping;
+import jalview.schemabinding.version2.MappingChoice;
+import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PdbentryItem;
+import jalview.schemabinding.version2.Pdbids;
+import jalview.schemabinding.version2.Property;
+import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequenceSet;
+import jalview.schemabinding.version2.SequenceSetProperties;
+import jalview.schemabinding.version2.Setting;
+import jalview.schemabinding.version2.StructureState;
+import jalview.schemabinding.version2.ThresholdLine;
+import jalview.schemabinding.version2.Tree;
+import jalview.schemabinding.version2.UserColours;
+import jalview.schemabinding.version2.Viewport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Unmarshaller;
+
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
.startsWith(
jmol.jmb.pdbentry[peid].getId()
.toLowerCase())))
+ {
continue;
+ }
if (matchedFile == null)
{
matchedFile = jmol.jmb.pdbentry[peid].getFile();
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
-
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
AnnotationElement ae;
if (aa[i].annotations != null)
{
ae = new AnnotationElement();
if (aa[i].annotations[a].description != null)
+ {
ae.setDescription(aa[i].annotations[a].description);
+ }
if (aa[i].annotations[a].displayCharacter != null)
+ {
ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ }
if (!Float.isNaN(aa[i].annotations[a].value))
+ {
ae.setValue(aa[i].annotations[a].value);
+ }
ae.setPosition(a);
if (aa[i].annotations[a].secondaryStructure != ' '
&& aa[i].annotations[a].secondaryStructure != '\0')
+ {
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
+ }
if (aa[i].annotations[a].colour != null
&& aa[i].annotations[a].colour != java.awt.Color.black)
errorMessage = null;
}
- Hashtable alreadyLoadedPDB;
+ Hashtable<String, String> alreadyLoadedPDB;
/**
* when set, local views will be updated from view stored in JalviewXML
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
if (alreadyLoadedPDB == null)
+ {
alreadyLoadedPDB = new Hashtable();
+ }
if (alreadyLoadedPDB.containsKey(pdbId))
+ {
return alreadyLoadedPDB.get(pdbId).toString();
+ }
try
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
-
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance)
+ .registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
// in principle Visible should always be true for annotation displayed
// in multiple views
if (an[i].hasVisible())
+ {
jda.visible = an[i].getVisible();
+ }
al.addAnnotation(jda);
anpos = ae[aa].getPosition();
if (anpos >= anot.length)
+ {
continue;
+ }
anot[anpos] = new jalview.datamodel.Annotation(
jaa.setScore(an[i].getScore());
}
if (an[i].hasVisible())
+ {
jaa.visible = an[i].getVisible();
+ }
if (an[i].hasCentreColLabels())
+ {
jaa.centreColLabels = an[i].getCentreColLabels();
+ }
if (an[i].hasScaleColLabels())
{
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
-
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
+ {
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
setting.getType(), setting.getOrder());
+ }
else
+ {
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
setting.getType(),
fs / jms.getFeatureSettings().getSettingCount());
+ }
if (setting.getDisplay())
{
af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
}
}
else
+ {
Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
}
}
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-import jalview.binding.*;
-import jalview.schemes.*;
+import jalview.binding.Annotation;
+import jalview.binding.AnnotationElement;
+import jalview.binding.Features;
+import jalview.binding.JGroup;
+import jalview.binding.JSeq;
+import jalview.binding.JalviewModel;
+import jalview.binding.JalviewModelSequence;
+import jalview.binding.Pdbids;
+import jalview.binding.Sequence;
+import jalview.binding.SequenceSet;
+import jalview.binding.Setting;
+import jalview.binding.Tree;
+import jalview.binding.UserColours;
+import jalview.binding.Viewport;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
+import java.io.InputStreamReader;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+
+import javax.swing.JOptionPane;
+
+import org.exolab.castor.xml.IDResolver;
+
/**
* DOCUMENT ME!
*
InputStreamReader in = new InputStreamReader(jin, "UTF-8");
JalviewModel object = new JalviewModel();
- object = (JalviewModel) object.unmarshal(in);
+ object = object.unmarshal(in);
af = LoadFromObject(object, file);
entryCount++;
entry.setId(ids[p].getId());
entry.setType(ids[p].getType());
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(entry);
}
}
for (int s = 0; s < ids.length; s++)
{
- seqs.addElement((jalview.datamodel.SequenceI) seqids
+ seqs.addElement(seqids
.elementAt(ids[s]));
}
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
-import java.util.HashMap;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
JMenu outputMenu = new JMenu();
- JMenu showAnnotationsMenu = new JMenu();
+ JMenu seqShowAnnotationsMenu = new JMenu();
- JMenu hideAnnotationsMenu = new JMenu();
+ JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem addReferenceAnnotations = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
+
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem();
JMenuItem sequenceFeature = new JMenuItem();
/*
* Build menus for annotation types that may be shown or hidden, and for
- * 'reference annotations' that may be added to the alignment. The scope is
- * annotations for the current selection group (if there is one), else the
- * current sequence (if there is one), else not applicable (e.g. for popup
- * menu within the sequence).
+ * 'reference annotations' that may be added to the alignment. First for the
+ * currently selected sequence (if there is one):
*/
- final List<SequenceI> sequenceScope = getSequenceScope(seq);
- if (!sequenceScope.isEmpty())
- {
- buildAnnotationTypesMenus(sequenceScope);
- configureReferenceAnnotationsMenu(addReferenceAnnotations, sequenceScope);
- }
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()
+ .getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
try
{
}
/**
- * Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
* "All" is added first, followed by a separator. Then add any annotation
- * types associated with the current selection.
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
* <p>
* Some annotation rows are always rendered together - these can be identified
* by a common graphGroup property > -1. Only one of each group will be marked
* <p>
* IUPredWS (Long), IUPredWS (Short)
*
- * @param forSequences
+ * @param seq
*/
- protected void buildAnnotationTypesMenus(List<SequenceI> forSequences)
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
+ List<SequenceI> forSequences)
{
- showAnnotationsMenu.removeAll();
- hideAnnotationsMenu.removeAll();
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
- addAnnotationTypeToShowHide(showAnnotationsMenu, forSequences, "", all,
- true, true);
- addAnnotationTypeToShowHide(hideAnnotationsMenu, forSequences, "", all,
- true, false);
- showAnnotationsMenu.addSeparator();
- hideAnnotationsMenu.addSeparator();
+ 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.
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
*/
- Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+ 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),
{
for (List<String> type : hiddenTypes.get(calcId))
{
- addAnnotationTypeToShowHide(showAnnotationsMenu, forSequences,
+ addAnnotationTypeToShowHide(showMenu, forSequences,
calcId, type, false, true);
}
}
// grey out 'show annotations' if none are hidden
- showAnnotationsMenu.setEnabled(!hiddenTypes.isEmpty());
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
for (String calcId : shownTypes.keySet())
{
for (List<String> type : shownTypes.get(calcId))
{
- addAnnotationTypeToShowHide(hideAnnotationsMenu, forSequences,
+ addAnnotationTypeToShowHide(hideMenu, forSequences,
calcId, type, false, false);
}
}
// grey out 'hide annotations' if none are shown
- hideAnnotationsMenu.setEnabled(!shownTypes.isEmpty());
+ hideMenu.setEnabled(!shownTypes.isEmpty());
}
/**
});
outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ "...");
- showAnnotationsMenu.setText(MessageManager
+ seqShowAnnotationsMenu.setText(MessageManager
.getString("label.show_annotations"));
- hideAnnotationsMenu.setText(MessageManager
+ seqHideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ groupShowAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ groupHideAnnotationsMenu.setText(MessageManager
.getString("label.hide_annotations"));
sequenceFeature.setText(MessageManager
.getString("label.create_sequence_feature"));
// groupMenu.add(chooseAnnotations);
/*
- * Add show/hide annotations to either Selection menu (if a selection group
- * in force), else to the Sequence menu.
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
*/
- SequenceGroup sg = this.ap.av.getSelectionGroup();
- if (sg != null && sg.getSize() > 0)
- {
- groupMenu.add(showAnnotationsMenu);
- groupMenu.add(hideAnnotationsMenu);
- groupMenu.add(addReferenceAnnotations);
- }
- else
- {
- sequenceMenu.add(showAnnotationsMenu);
- sequenceMenu.add(hideAnnotationsMenu);
- sequenceMenu.add(addReferenceAnnotations);
- }
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true);
+ jalview.io.AppletFormatAdapter.FILE, sequence, true,
+ Desktop.instance);
}
}
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;
+ }
+
CommandI command = (CommandI) historyList.pop();
- command.undoCommand(af.getViewAlignments());
-
if (ap.av.historyList.contains(command))
{
+ command.undoCommand(af.getViewAlignments());
ap.av.historyList.remove(command);
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
package jalview.io;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
-import jalview.util.MessageManager;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
if ((al != null) && (al.getHeight() > 0))
{
+ for (SequenceI sq : al.getSequences())
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getPDBId() != null)
+ {
+ for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
+ }
if (viewport != null)
{
// TODO: create undo object for this JAL-1101
}
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
-
}
else
{
{ title }));
if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
alignFrame.setFileName(file, format);
+ }
if (raiseGUI)
{
// add the window to the GUI
-#Thu May 01 17:34:18 BST 2014
+#Fri Oct 31 16:47:51 GMT 2014
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.schemabinding.version2;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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;
-
- // ----------------/
- // - 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.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);
- }
-
- /**
- */
- 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 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getAnnotationElement",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
- }));
- }
-
- 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;
- }
-
- /**
- * 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();
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setAnnotationElement",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
- }));
- }
-
- 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;
- }
-
- /**
- * 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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
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;
+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);
}
- 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.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;
+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);
}
- 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);
- }
- 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);
+ //-- _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 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);
+ //-- _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.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);
+ //-- _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");
}
- }
-
- 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);
+ //-- _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: _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);
+ //-- _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);
}
- 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);
+ //-- _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: _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);
+ //-- _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.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);
+ //-- _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: _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);
+ //-- _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.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);
+ //-- _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: _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);
+ //-- _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);
}
- }
-
- 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);
+ //-- _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);
}
- 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);
+ //-- _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: _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);
+ //-- _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 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);
+ //-- _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: _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);
+ //-- _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 (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);
+ //-- 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: _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;
+ 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.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);
+ //-- _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: _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);
+ //-- _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
}
- 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);
+ //-- _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
}
- }
-
- 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);
}
- 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);
- }
- 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);
- }
+ //-----------/
+ //- Methods -/
+ //-----------/
- 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)
- {
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
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);
- }
-
- 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);
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
}
- 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");
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.Annotation.class;
}
- 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
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
}
- 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");
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
}
- 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");
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
}
- 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
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName(
+ ) {
+ return _xmlName;
}
- 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;
- }
+ /**
+ * 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 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");
}
- }
-
- 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());
+ 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 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
+
}
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
- }
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- }
+ /**
+ * 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 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 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 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 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 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 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;
- }
+ /**
+ * 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;
+ }
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
GraphLine annotationThreshold;
- float r1, g1, b1, rr, gg, bb, dr, dg, db;
+ float r1, g1, b1, rr, gg, bb;
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
acg.rr = rr;
acg.gg = gg;
acg.bb = bb;
- acg.dr = dr;
- acg.dg = dg;
- acg.db = db;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
-
+ acg.noGradient = noGradient;
return acg;
}
{
annotationThreshold = annotation.threshold;
}
+ // clear values so we don't get weird black bands...
+ r1 = 254;
+ g1 = 254;
+ b1 = 254;
+ rr = 0;
+ gg = 0;
+ bb = 0;
+
+ noGradient = true;
}
/**
rr = maxColour.getRed() - r1;
gg = maxColour.getGreen() - g1;
bb = maxColour.getBlue() - b1;
+
+ noGradient = false;
}
@Override
&& annotation.annotations[j] != null
&& !jalview.util.Comparison.isGap(c))
{
+ Annotation aj = annotation.annotations[j];
+ // 'use original colours' => colourScheme != null
+ // -> look up colour to be used
+ // predefined colours => preconfigured shading
+ // -> only use original colours reference if thresholding enabled &
+ // minmax exists
+ // annotation.hasIcons => null or black colours replaced with glyph
+ // colours
+ // -> reuse original colours if present
+ // -> if thresholding enabled then return colour on non-whitespace glyph
- if (annotation.annotations[j].colour != null)
- {
- if (predefinedColours || annotation.hasIcons)
- {
- return annotation.annotations[j].colour;
- }
- }
- else
- {
- if (predefinedColours)
- {
- return currentColour;
- }
- }
if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
- || (annotationThreshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+ || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+ : aj.value <= annotationThreshold.value)))
{
-
- float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
- {
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
- }
- else if (thresholdIsMinMax && annotation.threshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
+ if (predefinedColours && aj.colour != null)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
+ currentColour = aj.colour;
}
- else
+ else if (annotation.hasIcons
+ && annotation.graph == AlignmentAnnotation.NO_GRAPH)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
+ {
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+ : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ else
+ {
+ //
+ return Color.white;
+ }
}
-
- if (colourScheme != null)
+ else if (noGradient)
{
- currentColour = colourScheme.findColour(c, j, seq);
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ if (aj.colour != null)
+ {
+ currentColour = aj.colour;
+ }
+ }
}
else
{
- dr = rr * range + r1;
- dg = gg * range + g1;
- db = bb * range + b1;
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
+ {
+ range = (annotation.annotations[j].value - annotation.threshold.value)
+ / (annotation.graphMax - annotation.threshold.value);
+ }
+ else if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && annotation.annotations[j].value >= annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+
+ currentColour = new Color(dr, dg, db);
- currentColour = new Color((int) dr, (int) dg, (int) db);
}
}
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
}
}
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
return currentColour;
}
*/
package jalview.structure;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
public class StructureMapping
{
}
return -1;
}
+
+ /**
+ * transfer a copy of an alignment annotation row in the PDB chain coordinate
+ * system onto the mapped sequence
+ *
+ * @param ana
+ * @return the copy that was remapped to the mapped sequence
+ * @note this method will create a copy and add it to the dataset sequence for
+ * the mapped sequence as well as the mapped sequence (if it is not a
+ * dataset sequence).
+ */
+ public AlignmentAnnotation transfer(AlignmentAnnotation ana)
+ {
+ AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
+ SequenceI ds = sequence;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ala_copy.remap(ds, mapping, 0, -1, 1);
+ ds.addAlignmentAnnotation(ala_copy);
+ if (ds != sequence)
+ {
+ // mapping wasn't to an original dataset sequence, so we make a copy on
+ // the mapped sequence too
+ ala_copy = new AlignmentAnnotation(ala_copy);
+ sequence.addAlignmentAnnotation(ala_copy);
+ }
+ return ala_copy;
+ }
}
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
import java.io.PrintStream;
import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.Vector;
}
}
- Hashtable mappingData = new Hashtable();
+ /**
+ * map between the PDB IDs (or structure identifiers) used by Jalview and the
+ * absolute filenames for PDB data that corresponds to it
+ */
+ HashMap<String, String> pdbIdFileName = new HashMap<String, String>(),
+ pdbFileNameId = new HashMap<String, String>();
+
+ public void registerPDBFile(String idForFile, String absoluteFile)
+ {
+ pdbIdFileName.put(idForFile, absoluteFile);
+ pdbFileNameId.put(absoluteFile, idForFile);
+ }
+
+ public String findIdForPDBFile(String idOrFile)
+ {
+ String id = pdbFileNameId.get(idOrFile);
+ return id;
+ }
+
+ public String findFileForPDBId(String idOrFile)
+ {
+ String id = pdbIdFileName.get(idOrFile);
+ return id;
+ }
+
+ public boolean isPDBFileRegistered(String idOrFile)
+ {
+ return pdbFileNameId.containsKey(idOrFile)
+ || pdbIdFileName.containsKey(idOrFile);
+ }
private static StructureSelectionManager nullProvider = null;
}
/**
+ * Import structure data and register a structure mapping for broadcasting
+ * colouring, mouseovers and selection events (convenience wrapper).
+ *
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, String protocol)
+ {
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ }
+
+ /**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ synchronized public MCview.PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
/*
*/
MCview.PDBfile pdb = null;
boolean parseSecStr=true;
- for (SequenceI sq:sequence)
+ if (isPDBFileRegistered(pdbFile))
{
- SequenceI ds = sq;while (ds.getDatasetSequence()!=null) { ds = ds.getDatasetSequence();};
- if (ds.getAnnotation()!=null)
+ for (SequenceI sq : sequence)
{
- for (AlignmentAnnotation ala:ds.getAnnotation())
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
{
- // false if any annotation present from this structure
- if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(), pdbFile))
+ for (AlignmentAnnotation ala : ds.getAnnotation())
{
- parseSecStr = false;
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (MCview.PDBfile.isCalcIdForFile(ala,
+ findIdForPDBFile(pdbFile)))
+ {
+ parseSecStr = false;
+ }
}
}
}
try
{
pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
-
+ if (pdb.id != null && pdb.id.trim().length() > 0
+ && FormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.id.trim(), pdbFile);
+ }
} catch (Exception ex)
{
ex.printStackTrace();
boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
- PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+ PDBChain chain = (pdb.chains.elementAt(i));
if (targetChain.length() > 0 && !targetChain.equals(chain.id)
&& !infChain)
{
// TODO: correctly determine sequence type for mixed na/peptide
// structures
AlignSeq as = new AlignSeq(sequence[s],
- ((PDBChain) pdb.chains.elementAt(i)).sequence,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ pdb.chains.elementAt(i).sequence,
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
: AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
index++;
} while (index < maxChain.atoms.size());
- if (mappings == null)
- {
- mappings = new StructureMapping[1];
- }
- else
- {
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
- }
-
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
pdbFile = "INLINE" + pdb.id;
}
-
- mappings[mappings.length - 1] = new StructureMapping(sequence[s],
+ StructureMapping newMapping = new StructureMapping(sequence[s],
pdbFile, pdb.id, maxChainId, mapping,
mappingDetails.toString());
- maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
+ if (forStructureView)
+ {
+
+ if (mappings == null)
+ {
+ mappings = new StructureMapping[1];
+ }
+ else
+ {
+ StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
+ System.arraycopy(mappings, 0, tmp, 0, mappings.length);
+ mappings = tmp;
+ }
+
+ mappings[mappings.length - 1] = newMapping;
+ }
+ maxChain.transferResidueAnnotation(newMapping);
}
// ///////
listeners.clear();
listeners = null;
}
- if (mappingData != null)
+ if (pdbIdFileName != null)
{
- mappingData.clear();
- mappingData = null;
+ pdbIdFileName.clear();
+ pdbIdFileName = null;
}
if (sel_listeners != null)
{
}
}
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
}
package jalview.datamodel;
-import static org.junit.Assert.*;
-
-import java.awt.Frame;
-
-import javax.swing.JFrame;
-import javax.swing.SwingWorker;
-
+import static org.junit.Assert.assertEquals;
import jalview.analysis.AlignSeq;
-import jalview.gui.AlignFrame;
import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
import org.junit.Test;
public class AlignmentAnnotationTests
{
+ @Test
+ public void testCopyConstructor()
+ {
+ SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
+ createAnnotation(sq);
+ AlignmentAnnotation alc, alo = sq.getAnnotation()[0];
+ alc = new AlignmentAnnotation(alo);
+ for (String key : alo.getProperties())
+ {
+ assertEquals("Property mismatch", alo.getProperty(key),
+ alc.getProperty(key));
+ }
+ }
/**
* create some dummy annotation derived from the sequence
*
for (int i = 0; i < al.length; i++)
{
al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
- (char) 0, (float) sq.findPosition(i)));
+ (char) 0, sq.findPosition(i)));
}
AlignmentAnnotation alan = new AlignmentAnnotation("For "
+ sq.getName(), "Fake alignment annot", al);
// create a sequence mapping for the annotation vector in its current state
alan.createSequenceMapping(sq, sq.getStart(), false);
+ alan.setProperty("CreatedBy", "createAnnotation");
sq.addAlignmentAnnotation(alan);
}
import jalview.io.AppletFormatAdapter;
import jalview.util.MessageManager;
+import java.awt.Component;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
+import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JSeparator;
import org.junit.Before;
import org.junit.Test;
public void testConfigureReferenceAnnotationsMenu()
{
JMenuItem menu = new JMenuItem();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
-
- seqs = parentPanel.getAlignment().getSequences();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
// make up new annotations and add to dataset sequences
// PDB.secondary structure on Sequence0
String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
assertEquals(expected, menu.getToolTipText());
}
+
+ /**
+ * Test for building menu options including 'show' and 'hide' annotation
+ * types.
+ */
+ @Test
+ public void testBuildAnnotationTypesMenus()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", 0);
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // JMOL.secondary structure on Sequence0 - hidden
+ annotation = new AlignmentAnnotation("secondary structure", "", 0);
+ annotation.setCalcId("JMOL");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // Jpred.SSP on Sequence0 - hidden
+ annotation = new AlignmentAnnotation("SSP", "", 0);
+ annotation.setCalcId("JPred");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", 0);
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to show "secondary structure" and "SSP", and to hide
+ * "secondary structure" and "Temp". Tooltip should be calcId.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertTrue(showMenu.isEnabled());
+ assertTrue(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(4, showOptions.length); // includes 'All' and separator
+ assertEquals(4, hideOptions.length);
+ assertEquals("All",
+ ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) showOptions[2]).getText());
+ assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
+ assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
+ assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
+
+ assertEquals("All",
+ ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) hideOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
+ }
+
+ /**
+ * Test for building menu options with only 'hide' annotation types enabled.
+ */
+ @Test
+ public void testBuildAnnotationTypesMenus_showDisabled()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", 0);
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", 0);
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to hide "secondary structure" and "Temp". Tooltip
+ * should be calcId. 'Show' menu should be disabled.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertFalse(showMenu.isEnabled());
+ assertTrue(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(2, showOptions.length); // includes 'All' and separator
+ assertEquals(4, hideOptions.length);
+ assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+
+ assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) hideOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
+ }
+
+ /**
+ * Test for building menu options with only 'show' annotation types enabled.
+ */
+ @Test
+ public void testBuildAnnotationTypesMenus_hideDisabled()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", 0);
+ annotation.setCalcId("PDB");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", 0);
+ annotation.setCalcId("PDB2");
+ annotation.visible = false;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to show "secondary structure" and "Temp". Tooltip
+ * should be calcId. 'hide' menu should be disabled.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertTrue(showMenu.isEnabled());
+ assertFalse(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(4, showOptions.length); // includes 'All' and separator
+ assertEquals(2, hideOptions.length);
+ assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) showOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
+ assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
+
+ assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ }
}
AlignmentI al;
- String pdbStr = "examples/2GIS.pdb";
+ String pdbStr = "examples/1gaq.txt";
String pdbId;
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
public void testJalviewProjectRelocationAnnotation() throws Exception
{
- String inFile = "examples/2GIS.pdb";
+ String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
&& MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
+ if (MCview.PDBfile.isCalcIdForFile(ana,
pdbentry.getId()))
{
found = true;
--- /dev/null
+package jalview.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+public class Mapping
+{
+
+ @Test
+ public void testPDBentryMapping() throws Exception
+ {
+ Sequence sq = new Sequence(
+ "1GAQ A subseq 126 to 219",
+ "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
+ Sequence sq1 = new Sequence(sq);
+ String inFile;
+ StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ // Associate the 1GAQ pdb file with the subsequence 'imported' from another
+ // source
+ PDBfile pde = ssm.setMapping(true, new SequenceI[]
+ { sq }, new String[]
+ { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+ assertTrue("PDB File couldn't be found", pde != null);
+ StructureMapping[] mp = ssm.getMapping(inFile);
+ assertTrue("No mappings made.", mp != null && mp.length > 0);
+ int nsecStr = 0, nsTemp = 0;
+ // test for presence of transferred annotation on sequence
+ for (AlignmentAnnotation alan : sq.getAnnotation())
+ {
+ if (alan.hasIcons)
+ {
+ nsecStr++;
+ }
+ if (alan.graph == alan.LINE_GRAPH)
+ {
+ nsTemp++;
+ }
+ }
+ assertEquals(
+ "Only one secondary structure should be transferred to associated sequence.",
+ 1, nsecStr);
+ assertEquals(
+ "Only two line graphs should be transferred to associated sequence.",
+ 2, nsTemp);
+ // Now test the transfer function and compare annotated positions
+ for (StructureMapping origMap:mp)
+ {
+ if (origMap.getSequence()==sq)
+ {
+ assertEquals("Mapping was incomplete.", sq.getLength() - 1,
+ (origMap.getPDBResNum(sq.getEnd()) - origMap
+ .getPDBResNum(sq.getStart())));
+ // sanity check - if this fails, mapping from first position in sequence
+ // we want to transfer to is not where we expect
+ assertEquals(1, origMap.getSeqPos(126));
+ SequenceI firstChain = pde.getSeqs().get(0);
+ // Compare the annotated positions on the PDB chain sequence with the
+ // annotation on the associated sequence
+ for (AlignmentAnnotation alan : firstChain.getAnnotation())
+ {
+ AlignmentAnnotation transfer = origMap.transfer(alan);
+ System.out.println("pdb:" + firstChain.getSequenceAsString());
+ System.out.println("ann:" + alan.toString());
+ System.out.println("pdb:" + sq.getSequenceAsString());
+ System.out.println("ann:" + transfer.toString());
+
+ for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
+ {
+ // walk along the pdb chain's jalview sequence
+ int rseqpos;
+ int fpos = origMap.getSeqPos(rseqpos = firstChain
+ .findPosition(p));
+ // only look at positions where there is a corresponding position in
+ // mapping
+ if (fpos < 1)
+ {
+ continue;
+ }
+ // p is index into PDB residue entries
+ // rseqpos is pdb sequence position for position p
+ // fpos is sequence position for associated position for rseqpos
+ int tanpos = sq.findIndex(fpos);
+ if (transfer.annotations.length <= tanpos)
+ {
+ // gone beyond mapping to the sequence
+ break;
+ }
+ Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
+ assertEquals("Non-equivalent annotation element at " + p + "("
+ + rseqpos + ")"
+ + " expected at " + fpos + " (alIndex "
+ + sq.findIndex(fpos) + ")",
+ a == null ? a : a.toString(),
+ b == null ? b : b.toString());
+ System.out.print("(" + a + "|" + b + ")");
+ }
+
+ }
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff