<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
<taskdef name="castor-srcgen"
- classname="org.exolab.castor.tools.ant.taskdefs.CastorSourceGenTask"
- classpathref="build.classpath" />
+ classname="org.castor.anttask.CastorCodeGenTask"
+ classpathref="build.classpath" />
<delete>
- <fileset dir="${sourceDir}/jalview/schemabinding/version2/">
- <filename name="*"/>
+ <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <include name="*.java"/>
+ <include name="descriptors/*.java"/>
</fileset>
</delete>
<castor-srcgen file="${schemaDir}/vamsas.xsd"
todir="${sourceDir}"
package="jalview.schemabinding.version2"
- warnings="true"
+ warnings="false"
nodesc="false"
+ verbose="true"
properties="${schemaDir}/jalview.properties"
/>
<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
todir="${sourceDir}"
package="jalview.schemabinding.version2"
- warnings="true"
+ warnings="false"
nodesc="false"
+ verbose="true"
properties="${schemaDir}/jalview.properties"
/>
<castor-srcgen file="${schemaDir}/jalview.xsd"
todir="${sourceDir}"
package="jalview.schemabinding.version2"
- warnings="true"
+ warnings="false"
nodesc="false"
+ verbose="true"
properties="${schemaDir}/jalview.properties"
/>
import jalview.bin.Cache;
import jalview.io.VamsasDatastore;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasFile;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.test.simpleclient.ArchiveClient;
-import org.vamsas.test.simpleclient.ClientDoc;
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+import uk.ac.vamsas.test.simpleclient.ArchiveClient;
+import uk.ac.vamsas.test.simpleclient.ClientDoc;
/**
* @author jimp
watchForChange = true;
if (watcher != null)
{
- watcher.start();
+ startWatcher(); /// TODO: check this works... must recreate watcher to start it...
}
// collect all uncached alignments and put them into the vamsas dataset.
// store them.
private Entry baseProvEntry()
{
- org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry();
+ uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
pentry.setUser(this.getProvenanceUser());
pentry.setApp(this.getClientHandle().getClientName());
pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
import java.util.IdentityHashMap;
import java.util.Vector;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.objects.core.Alignment;
-import org.vamsas.objects.core.AlignmentSequence;
-import org.vamsas.objects.core.AlignmentSequenceAnnotation;
-import org.vamsas.objects.core.AnnotationElement;
-import org.vamsas.objects.core.DataSet;
-import org.vamsas.objects.core.DataSetAnnotations;
-import org.vamsas.objects.core.DbRef;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.Glyph;
-import org.vamsas.objects.core.Input;
-import org.vamsas.objects.core.Link;
-import org.vamsas.objects.core.Newick;
-import org.vamsas.objects.core.Param;
-import org.vamsas.objects.core.Property;
-import org.vamsas.objects.core.Provenance;
-import org.vamsas.objects.core.RangeAnnotation;
-import org.vamsas.objects.core.RangeType;
-import org.vamsas.objects.core.Seg;
-import org.vamsas.objects.core.Sequence;
-import org.vamsas.objects.core.Tree;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.test.simpleclient.ClientDoc;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Input;
+import uk.ac.vamsas.objects.core.Link;
+import uk.ac.vamsas.objects.core.Newick;
+import uk.ac.vamsas.objects.core.Param;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.Tree;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.test.simpleclient.ClientDoc;
/*
*
* @param vobj
* @return Jalview datamodel object bound to the vamsas document object
*/
- protected Object getvObj2jv(org.vamsas.client.Vobject vobj)
+ protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
{
VorbaId id = vobj.getVorbaId();
if (id == null)
return null;
}
- protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj)
+ protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
{
VorbaId id = vobj.getVorbaId();
if (id == null)
// this *will* break when alignment contains both nucleotide and amino
// acid sequences.
String dict = jal.isNucleotide() ?
- org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
- : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
for (int i = 0; i < jal.getHeight(); i++)
{
SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
else
{
// todo: verify and update mutable alignment props.
- if (alignment.getModifiable())
+ if (alignment.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS
{
System.out.println("update alignment in document.");
}
}
if (aa[i].sequenceRef != null)
{
- org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.
+ uk.ac.vamsas.objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
- org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.
vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[
i]);
int[] gapMap = null;
}
if (an == null)
{
- an = new org.vamsas.objects.core.AlignmentSequenceAnnotation();
+ an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
Seg vSeg = new Seg();
vSeg.setStart(1);
vSeg.setInclusive(true);
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.
+ .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.
PROTEIN_SS_3STATE);
ss.setContent(String
.valueOf(aa[i].annotations[a].
else
{
// update reference sequence Annotation
- if (an.getModifiable())
+ if (an.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
// verify existing alignment sequence annotation is up to date
System.out.println("update alignment sequence annotation.");
else
{
// add Alignment Annotation
- org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.
+ uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.
objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
if (an == null)
{
- an = new org.vamsas.objects.core.AlignmentAnnotation();
+ an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
an.setType("jalview:AnnotationRow");
an.setDescription(aa[i].description);
alignment.addAlignmentAnnotation(an);
{
Glyph ss = new Glyph();
ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.
+ .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.
PROTEIN_SS_3STATE);
ss.setContent(String
.valueOf(aa[i].annotations[a].
if (aa[i].editable)
{
//an.addProperty(newProperty("jalview:editable", null, "true"));
- an.setModifiable(true);
+ // an.setModifiable(""); // TODO: This is not the way the modifiable flag is supposed to be used.
}
if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
{
}
else
{
- if (an.getModifiable())
+ if (an.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
// verify annotation - update (perhaps)
Cache.log.info(
}
else
{
- if (tree.getModifiable())
+ if (tree.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
// verify any changes.
System.out.println("Update tree in document.");
}
// LATER: deal sensibly with multiple inputs.
Input vInput = tp.getEntry(pe).getInput(0);
- if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)
+ if (vInput.getObjRef() instanceof uk.ac.vamsas.objects.core.Alignment)
{
// recover an AlignmentView for the input data
- AlignViewport javport = (AlignViewport) getvObj2jv( (org.vamsas.
+ AlignViewport javport = (AlignViewport) getvObj2jv( (uk.ac.vamsas.
client.Vobject) vInput
.getObjRef());
jalview.datamodel.AlignmentI jal = javport.getAlignment();
dsseq = new jalview.datamodel.Sequence(
dataset.getSequence(i).getName(),
dataset.getSequence(i).getSequence(),
- dataset.getSequence(i).getStart(),
- dataset.getSequence(i).getEnd());
+ (int)dataset.getSequence(i).getStart(),
+ (int)dataset.getSequence(i).getEnd());
dsseq.setDescription(dataset.getSequence(i).getDescription());
bindjvvobj(dsseq, dataset.getSequence(i));
dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
{
- org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
+ uk.ac.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
al);
AlignViewport av = (AlignViewport) getvObj2jv(alignment);
jalview.datamodel.AlignmentI jal = null;
alseq = new jalview.datamodel.Sequence(
valseq.getName(),
valseq.getSequence().replace(valGapchar, gapChar),
- valseq.getStart(),
- valseq.getEnd());
+ (int)valseq.getStart(),
+ (int)valseq.getEnd());
Vobject datsetseq = (Vobject) valseq.getRefid();
if (datsetseq != null)
else
{
// update existing annotation - can do this in place
- if (vasannot[a].getModifiable())
+ if (vasannot[a].getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
Cache.log.info(
"UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// ////////////////////////////////////
if (alignment.getAlignmentAnnotationCount() > 0)
{
- org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
+ uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
getAlignmentAnnotation();
for (int j = 0; j < an.length; j++)
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place.
Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
- if (an[j].getModifiable())
+ if (an[j].getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
// TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
Cache.log.info(
* @param annotation
* @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
*/
- private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation
+ private Object[] parseRangeAnnotation(uk.ac.vamsas.objects.core.RangeAnnotation
annotation)
{
// set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
AnnotationElement ae[] = annotation.getAnnotationElement();
for (int aa = 0; aa < ae.length; aa++)
{
- int pos = ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1)
+ int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1)
if (pos >= 0 && pos < rangeMap.length)
{
int row = ae[aa].getAfter() ? 1 : 0;
Glyph[] glyphs = ae[aa].getGlyph();
for (int g = 0; g < glyphs.length; g++)
{
- if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ if (glyphs[g].getDict().equals(uk.ac.vamsas.objects.utils.
GlyphDictionary.PROTEIN_SS_3STATE))
{
ss = glyphs[g].getContent();
AeContent[HASSECSTR] = true;
}
- else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ else if (glyphs[g].getDict().equals(uk.ac.vamsas.objects.utils.
GlyphDictionary.
PROTEIN_HD_HYDRO))
{
c == '-' ? 255 : 0);
}
- else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ else if (glyphs[g].getDict().equals(uk.ac.vamsas.objects.utils.
GlyphDictionary.DEFAULT))
{
dc = glyphs[g].getContent();
*/
private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.
datamodel.AlignmentI jal,
- org.vamsas.objects.core.RangeAnnotation annotation)
+ uk.ac.vamsas.objects.core.RangeAnnotation annotation)
{
jalview.datamodel.AlignmentAnnotation jan = null;
if (annotation == null)
{
return null;
}
- // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);
- //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));
+ // boolean hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
+ //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
/*int se[] = getBounds(annotation);
if (se==null)
se=new int[] {0,jal.getWidth()-1};
parsedRangeAnnotation[2];
boolean[] has = (boolean[]) parsedRangeAnnotation[0];
// VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant
- /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
- || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
+ /*if ((annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) && ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
+ || (hasSequenceRef=true && ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
*/
if (has[HASVALS])
{
Cache.log.warn("Ignoring " + annotation.getLinkCount() +
"links added to AlignmentAnnotation.");
}
- if (annotation.getModifiable())
+ if (annotation.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
{
jan.editable = true;
}
if (annotation.getPropertyCount() > 0)
{
// look for special jalview properties
- org.vamsas.objects.core.Property[] props = annotation.getProperty();
+ uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
for (int p = 0; p < props.length; p++)
{
if (props[p].getName().equalsIgnoreCase("jalview:graphType"))
--- /dev/null
+#Tue May 15 19:58:04 BST 2007\r
+jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor\r
+jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor\r
+jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor\r
+jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor\r
+jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
+jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
+jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
+jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor\r
+jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor\r
+jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
+jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
+jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor\r
+jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
+jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor\r
+jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor\r
+jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor\r
+jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
+jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor\r
+jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor\r
+jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
+jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
+jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor\r
+jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor\r
+jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
+jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor\r
+jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor\r
+jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor\r
+jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor\r
+jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor\r
+jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
+jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor\r
+jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Annotation.\r
//--------------------------/\r
\r
/**\r
- * Field _graph\r
+ * Field _graph.\r
*/\r
private boolean _graph;\r
\r
private boolean _has_graph;\r
\r
/**\r
- * Field _graphType\r
+ * Field _graphType.\r
*/\r
private int _graphType;\r
\r
private boolean _has_graphType;\r
\r
/**\r
- * Field _sequenceRef\r
+ * Field _sequenceRef.\r
*/\r
private java.lang.String _sequenceRef;\r
\r
/**\r
- * Field _graphColour\r
+ * Field _graphColour.\r
*/\r
private int _graphColour;\r
\r
private boolean _has_graphColour;\r
\r
/**\r
- * Field _graphGroup\r
+ * Field _graphGroup.\r
*/\r
private int _graphGroup;\r
\r
private boolean _has_graphGroup;\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private java.lang.String _id;\r
\r
/**\r
- * Field _scoreOnly\r
+ * Field _scoreOnly.\r
*/\r
private boolean _scoreOnly = false;\r
\r
private boolean _has_scoreOnly;\r
\r
/**\r
- * Field _score\r
+ * Field _score.\r
*/\r
private double _score;\r
\r
private boolean _has_score;\r
\r
/**\r
- * Field _visible\r
+ * Field _visible.\r
*/\r
private boolean _visible;\r
\r
private boolean _has_visible;\r
\r
/**\r
- * Field _annotationElementList\r
+ * Field _annotationElementList.\r
*/\r
private java.util.Vector _annotationElementList;\r
\r
/**\r
- * Field _label\r
+ * Field _label.\r
*/\r
private java.lang.String _label;\r
\r
/**\r
- * Field _description\r
+ * Field _description.\r
*/\r
private java.lang.String _description;\r
\r
/**\r
- * Field _thresholdLine\r
+ * Field _thresholdLine.\r
*/\r
private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
\r
\r
public Annotation() {\r
super();\r
- _annotationElementList = new Vector();\r
- } //-- jalview.schemabinding.version2.Annotation()\r
+ this._annotationElementList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addAnnotationElement\r
- * \r
* \r
* \r
* @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method addAnnotationElement\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.add(index, vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method deleteGraph\r
- * \r
*/\r
- public void deleteGraph()\r
- {\r
+ public void deleteGraph(\r
+ ) {\r
this._has_graph= false;\r
- } //-- void deleteGraph() \r
+ }\r
\r
/**\r
- * Method deleteGraphColour\r
- * \r
*/\r
- public void deleteGraphColour()\r
- {\r
+ public void deleteGraphColour(\r
+ ) {\r
this._has_graphColour= false;\r
- } //-- void deleteGraphColour() \r
+ }\r
\r
/**\r
- * Method deleteGraphGroup\r
- * \r
*/\r
- public void deleteGraphGroup()\r
- {\r
+ public void deleteGraphGroup(\r
+ ) {\r
this._has_graphGroup= false;\r
- } //-- void deleteGraphGroup() \r
+ }\r
\r
/**\r
- * Method deleteGraphType\r
- * \r
*/\r
- public void deleteGraphType()\r
- {\r
+ public void deleteGraphType(\r
+ ) {\r
this._has_graphType= false;\r
- } //-- void deleteGraphType() \r
+ }\r
\r
/**\r
- * Method deleteScore\r
- * \r
*/\r
- public void deleteScore()\r
- {\r
+ public void deleteScore(\r
+ ) {\r
this._has_score= false;\r
- } //-- void deleteScore() \r
+ }\r
\r
/**\r
- * Method deleteScoreOnly\r
- * \r
*/\r
- public void deleteScoreOnly()\r
- {\r
+ public void deleteScoreOnly(\r
+ ) {\r
this._has_scoreOnly= false;\r
- } //-- void deleteScoreOnly() \r
+ }\r
\r
/**\r
- * Method deleteVisible\r
- * \r
*/\r
- public void deleteVisible()\r
- {\r
+ public void deleteVisible(\r
+ ) {\r
this._has_visible= false;\r
- } //-- void deleteVisible() \r
+ }\r
\r
/**\r
- * Method enumerateAnnotationElement\r
+ * Method enumerateAnnotationElement.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AnnotationElement elements\r
*/\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
+ public java.util.Enumeration enumerateAnnotationElement(\r
+ ) {\r
+ return this._annotationElementList.elements();\r
+ }\r
\r
/**\r
- * Method getAnnotationElement\r
- * \r
- * \r
+ * Method getAnnotationElement.\r
* \r
* @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.AnnotationElement at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) \r
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotationElement\r
+ * Method getAnnotationElement.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
* \r
- * \r
- * \r
- * @return AnnotationElement\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() \r
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(\r
+ ) {\r
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];\r
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getAnnotationElementCount\r
- * \r
+ * Method getAnnotationElementCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
+ public int getAnnotationElementCount(\r
+ ) {\r
+ return this._annotationElementList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'description'.\r
* \r
- * @return String\r
- * @return the value of field 'description'.\r
+ * @return the value of field 'Description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription(\r
+ ) {\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ }\r
\r
/**\r
* Returns the value of field 'graph'.\r
* \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
+ * @return the value of field 'Graph'.\r
*/\r
- public boolean getGraph()\r
- {\r
+ public boolean getGraph(\r
+ ) {\r
return this._graph;\r
- } //-- boolean getGraph() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphColour'.\r
* \r
- * @return int\r
- * @return the value of field 'graphColour'.\r
+ * @return the value of field 'GraphColour'.\r
*/\r
- public int getGraphColour()\r
- {\r
+ public int getGraphColour(\r
+ ) {\r
return this._graphColour;\r
- } //-- int getGraphColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphGroup'.\r
* \r
- * @return int\r
- * @return the value of field 'graphGroup'.\r
+ * @return the value of field 'GraphGroup'.\r
*/\r
- public int getGraphGroup()\r
- {\r
+ public int getGraphGroup(\r
+ ) {\r
return this._graphGroup;\r
- } //-- int getGraphGroup() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphType'.\r
* \r
- * @return int\r
- * @return the value of field 'graphType'.\r
+ * @return the value of field 'GraphType'.\r
*/\r
- public int getGraphType()\r
- {\r
+ public int getGraphType(\r
+ ) {\r
return this._graphType;\r
- } //-- int getGraphType() \r
+ }\r
\r
/**\r
* Returns the value of field 'id'.\r
* \r
- * @return String\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId(\r
+ ) {\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ }\r
\r
/**\r
* Returns the value of field 'label'.\r
* \r
- * @return String\r
- * @return the value of field 'label'.\r
+ * @return the value of field 'Label'.\r
*/\r
- public java.lang.String getLabel()\r
- {\r
+ public java.lang.String getLabel(\r
+ ) {\r
return this._label;\r
- } //-- java.lang.String getLabel() \r
+ }\r
\r
/**\r
* Returns the value of field 'score'.\r
* \r
- * @return double\r
- * @return the value of field 'score'.\r
+ * @return the value of field 'Score'.\r
*/\r
- public double getScore()\r
- {\r
+ public double getScore(\r
+ ) {\r
return this._score;\r
- } //-- double getScore() \r
+ }\r
\r
/**\r
* Returns the value of field 'scoreOnly'.\r
* \r
- * @return boolean\r
- * @return the value of field 'scoreOnly'.\r
+ * @return the value of field 'ScoreOnly'.\r
*/\r
- public boolean getScoreOnly()\r
- {\r
+ public boolean getScoreOnly(\r
+ ) {\r
return this._scoreOnly;\r
- } //-- boolean getScoreOnly() \r
+ }\r
\r
/**\r
* Returns the value of field 'sequenceRef'.\r
* \r
- * @return String\r
- * @return the value of field 'sequenceRef'.\r
+ * @return the value of field 'SequenceRef'.\r
*/\r
- public java.lang.String getSequenceRef()\r
- {\r
+ public java.lang.String getSequenceRef(\r
+ ) {\r
return this._sequenceRef;\r
- } //-- java.lang.String getSequenceRef() \r
+ }\r
\r
/**\r
* Returns the value of field 'thresholdLine'.\r
* \r
- * @return ThresholdLine\r
- * @return the value of field 'thresholdLine'.\r
+ * @return the value of field 'ThresholdLine'.\r
*/\r
- public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
- {\r
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine(\r
+ ) {\r
return this._thresholdLine;\r
- } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() \r
+ }\r
\r
/**\r
* Returns the value of field 'visible'.\r
* \r
- * @return boolean\r
- * @return the value of field 'visible'.\r
+ * @return the value of field 'Visible'.\r
*/\r
- public boolean getVisible()\r
- {\r
+ public boolean getVisible(\r
+ ) {\r
return this._visible;\r
- } //-- boolean getVisible() \r
+ }\r
\r
/**\r
- * Method hasGraph\r
- * \r
- * \r
+ * Method hasGraph.\r
* \r
- * @return boolean\r
+ * @return true if at least one Graph has been added\r
*/\r
- public boolean hasGraph()\r
- {\r
+ public boolean hasGraph(\r
+ ) {\r
return this._has_graph;\r
- } //-- boolean hasGraph() \r
+ }\r
\r
/**\r
- * Method hasGraphColour\r
- * \r
- * \r
+ * Method hasGraphColour.\r
* \r
- * @return boolean\r
+ * @return true if at least one GraphColour has been added\r
*/\r
- public boolean hasGraphColour()\r
- {\r
+ public boolean hasGraphColour(\r
+ ) {\r
return this._has_graphColour;\r
- } //-- boolean hasGraphColour() \r
+ }\r
\r
/**\r
- * Method hasGraphGroup\r
+ * Method hasGraphGroup.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one GraphGroup has been added\r
*/\r
- public boolean hasGraphGroup()\r
- {\r
+ public boolean hasGraphGroup(\r
+ ) {\r
return this._has_graphGroup;\r
- } //-- boolean hasGraphGroup() \r
+ }\r
\r
/**\r
- * Method hasGraphType\r
- * \r
- * \r
+ * Method hasGraphType.\r
* \r
- * @return boolean\r
+ * @return true if at least one GraphType has been added\r
*/\r
- public boolean hasGraphType()\r
- {\r
+ public boolean hasGraphType(\r
+ ) {\r
return this._has_graphType;\r
- } //-- boolean hasGraphType() \r
+ }\r
\r
/**\r
- * Method hasScore\r
+ * Method hasScore.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Score has been added\r
*/\r
- public boolean hasScore()\r
- {\r
+ public boolean hasScore(\r
+ ) {\r
return this._has_score;\r
- } //-- boolean hasScore() \r
+ }\r
\r
/**\r
- * Method hasScoreOnly\r
- * \r
- * \r
+ * Method hasScoreOnly.\r
* \r
- * @return boolean\r
+ * @return true if at least one ScoreOnly has been added\r
*/\r
- public boolean hasScoreOnly()\r
- {\r
+ public boolean hasScoreOnly(\r
+ ) {\r
return this._has_scoreOnly;\r
- } //-- boolean hasScoreOnly() \r
+ }\r
\r
/**\r
- * Method hasVisible\r
+ * Method hasVisible.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Visible has been added\r
*/\r
- public boolean hasVisible()\r
- {\r
+ public boolean hasVisible(\r
+ ) {\r
return this._has_visible;\r
- } //-- boolean hasVisible() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Returns the value of field 'graph'.\r
* \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean isGraph(\r
+ ) {\r
+ return this._graph;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
* \r
+ * @return the value of field 'ScoreOnly'.\r
+ */\r
+ public boolean isScoreOnly(\r
+ ) {\r
+ return this._scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
+ * Returns the value of field 'visible'.\r
* \r
+ * @return the value of field 'Visible'.\r
+ */\r
+ public boolean isVisible(\r
+ ) {\r
+ return this._visible;\r
+ }\r
+\r
+ /**\r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllAnnotationElement\r
- * \r
*/\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
+ public void removeAllAnnotationElement(\r
+ ) {\r
+ this._annotationElementList.clear();\r
+ }\r
\r
/**\r
- * Method removeAnnotationElement\r
- * \r
+ * Method removeAnnotationElement.\r
* \r
+ * @param vAnnotationElement\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {\r
+ boolean removed = _annotationElementList.remove(vAnnotationElement);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElementAt.\r
* \r
* @param index\r
- * @return AnnotationElement\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
return (jalview.schemabinding.version2.AnnotationElement) obj;\r
- } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) \r
+ }\r
\r
/**\r
- * Method setAnnotationElement\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotationElement(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
}\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
+ \r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method setAnnotationElement\r
* \r
* \r
- * \r
- * @param annotationElementArray\r
+ * @param vAnnotationElementArray\r
*/\r
- public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)\r
- {\r
+ public void setAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {\r
//-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
+ _annotationElementList.clear();\r
+ \r
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
}\r
- } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \r
+ }\r
\r
/**\r
* Sets the value of field 'description'.\r
* \r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'graph'.\r
* \r
* @param graph the value of field 'graph'.\r
*/\r
- public void setGraph(boolean graph)\r
- {\r
+ public void setGraph(\r
+ final boolean graph) {\r
this._graph = graph;\r
this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphColour'.\r
* \r
* @param graphColour the value of field 'graphColour'.\r
*/\r
- public void setGraphColour(int graphColour)\r
- {\r
+ public void setGraphColour(\r
+ final int graphColour) {\r
this._graphColour = graphColour;\r
this._has_graphColour = true;\r
- } //-- void setGraphColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphGroup'.\r
* \r
* @param graphGroup the value of field 'graphGroup'.\r
*/\r
- public void setGraphGroup(int graphGroup)\r
- {\r
+ public void setGraphGroup(\r
+ final int graphGroup) {\r
this._graphGroup = graphGroup;\r
this._has_graphGroup = true;\r
- } //-- void setGraphGroup(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphType'.\r
* \r
* @param graphType the value of field 'graphType'.\r
*/\r
- public void setGraphType(int graphType)\r
- {\r
+ public void setGraphType(\r
+ final int graphType) {\r
this._graphType = graphType;\r
this._has_graphType = true;\r
- } //-- void setGraphType(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(\r
+ final java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'label'.\r
* \r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label)\r
- {\r
+ public void setLabel(\r
+ final java.lang.String label) {\r
this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'score'.\r
* \r
* @param score the value of field 'score'.\r
*/\r
- public void setScore(double score)\r
- {\r
+ public void setScore(\r
+ final double score) {\r
this._score = score;\r
this._has_score = true;\r
- } //-- void setScore(double) \r
+ }\r
\r
/**\r
* Sets the value of field 'scoreOnly'.\r
* \r
* @param scoreOnly the value of field 'scoreOnly'.\r
*/\r
- public void setScoreOnly(boolean scoreOnly)\r
- {\r
+ public void setScoreOnly(\r
+ final boolean scoreOnly) {\r
this._scoreOnly = scoreOnly;\r
this._has_scoreOnly = true;\r
- } //-- void setScoreOnly(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'sequenceRef'.\r
* \r
* @param sequenceRef the value of field 'sequenceRef'.\r
*/\r
- public void setSequenceRef(java.lang.String sequenceRef)\r
- {\r
+ public void setSequenceRef(\r
+ final java.lang.String sequenceRef) {\r
this._sequenceRef = sequenceRef;\r
- } //-- void setSequenceRef(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'thresholdLine'.\r
* \r
* @param thresholdLine the value of field 'thresholdLine'.\r
*/\r
- public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)\r
- {\r
+ public void setThresholdLine(\r
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine) {\r
this._thresholdLine = thresholdLine;\r
- } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) \r
+ }\r
\r
/**\r
* Sets the value of field 'visible'.\r
* \r
* @param visible the value of field 'visible'.\r
*/\r
- public void setVisible(boolean visible)\r
- {\r
+ public void setVisible(\r
+ final boolean visible) {\r
this._visible = visible;\r
this._has_visible = true;\r
- } //-- void setVisible(boolean) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Annotation\r
+ */\r
+ public static jalview.schemabinding.version2.Annotation unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class AnnotationColours.\r
//--------------------------/\r
\r
/**\r
- * Field _aboveThreshold\r
+ * Field _aboveThreshold.\r
*/\r
private int _aboveThreshold;\r
\r
private boolean _has_aboveThreshold;\r
\r
/**\r
- * Field _annotation\r
+ * Field _annotation.\r
*/\r
private java.lang.String _annotation;\r
\r
/**\r
- * Field _minColour\r
+ * Field _minColour.\r
*/\r
private int _minColour;\r
\r
private boolean _has_minColour;\r
\r
/**\r
- * Field _maxColour\r
+ * Field _maxColour.\r
*/\r
private int _maxColour;\r
\r
private boolean _has_maxColour;\r
\r
/**\r
- * Field _colourScheme\r
+ * Field _colourScheme.\r
*/\r
private java.lang.String _colourScheme;\r
\r
/**\r
- * Field _threshold\r
+ * Field _threshold.\r
*/\r
private float _threshold;\r
\r
\r
public AnnotationColours() {\r
super();\r
- } //-- jalview.schemabinding.version2.AnnotationColours()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteAboveThreshold\r
- * \r
*/\r
- public void deleteAboveThreshold()\r
- {\r
+ public void deleteAboveThreshold(\r
+ ) {\r
this._has_aboveThreshold= false;\r
- } //-- void deleteAboveThreshold() \r
+ }\r
\r
/**\r
- * Method deleteMaxColour\r
- * \r
*/\r
- public void deleteMaxColour()\r
- {\r
+ public void deleteMaxColour(\r
+ ) {\r
this._has_maxColour= false;\r
- } //-- void deleteMaxColour() \r
+ }\r
\r
/**\r
- * Method deleteMinColour\r
- * \r
*/\r
- public void deleteMinColour()\r
- {\r
+ public void deleteMinColour(\r
+ ) {\r
this._has_minColour= false;\r
- } //-- void deleteMinColour() \r
+ }\r
\r
/**\r
- * Method deleteThreshold\r
- * \r
*/\r
- public void deleteThreshold()\r
- {\r
+ public void deleteThreshold(\r
+ ) {\r
this._has_threshold= false;\r
- } //-- void deleteThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'aboveThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'aboveThreshold'.\r
+ * @return the value of field 'AboveThreshold'.\r
*/\r
- public int getAboveThreshold()\r
- {\r
+ public int getAboveThreshold(\r
+ ) {\r
return this._aboveThreshold;\r
- } //-- int getAboveThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'annotation'.\r
* \r
- * @return String\r
- * @return the value of field 'annotation'.\r
+ * @return the value of field 'Annotation'.\r
*/\r
- public java.lang.String getAnnotation()\r
- {\r
+ public java.lang.String getAnnotation(\r
+ ) {\r
return this._annotation;\r
- } //-- java.lang.String getAnnotation() \r
+ }\r
\r
/**\r
* Returns the value of field 'colourScheme'.\r
* \r
- * @return String\r
- * @return the value of field 'colourScheme'.\r
+ * @return the value of field 'ColourScheme'.\r
*/\r
- public java.lang.String getColourScheme()\r
- {\r
+ public java.lang.String getColourScheme(\r
+ ) {\r
return this._colourScheme;\r
- } //-- java.lang.String getColourScheme() \r
+ }\r
\r
/**\r
* Returns the value of field 'maxColour'.\r
* \r
- * @return int\r
- * @return the value of field 'maxColour'.\r
+ * @return the value of field 'MaxColour'.\r
*/\r
- public int getMaxColour()\r
- {\r
+ public int getMaxColour(\r
+ ) {\r
return this._maxColour;\r
- } //-- int getMaxColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'minColour'.\r
* \r
- * @return int\r
- * @return the value of field 'minColour'.\r
+ * @return the value of field 'MinColour'.\r
*/\r
- public int getMinColour()\r
- {\r
+ public int getMinColour(\r
+ ) {\r
return this._minColour;\r
- } //-- int getMinColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'threshold'.\r
* \r
- * @return float\r
- * @return the value of field 'threshold'.\r
+ * @return the value of field 'Threshold'.\r
*/\r
- public float getThreshold()\r
- {\r
+ public float getThreshold(\r
+ ) {\r
return this._threshold;\r
- } //-- float getThreshold() \r
+ }\r
\r
/**\r
- * Method hasAboveThreshold\r
- * \r
- * \r
+ * Method hasAboveThreshold.\r
* \r
- * @return boolean\r
+ * @return true if at least one AboveThreshold has been added\r
*/\r
- public boolean hasAboveThreshold()\r
- {\r
+ public boolean hasAboveThreshold(\r
+ ) {\r
return this._has_aboveThreshold;\r
- } //-- boolean hasAboveThreshold() \r
+ }\r
\r
/**\r
- * Method hasMaxColour\r
+ * Method hasMaxColour.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one MaxColour has been added\r
*/\r
- public boolean hasMaxColour()\r
- {\r
+ public boolean hasMaxColour(\r
+ ) {\r
return this._has_maxColour;\r
- } //-- boolean hasMaxColour() \r
+ }\r
\r
/**\r
- * Method hasMinColour\r
- * \r
+ * Method hasMinColour.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one MinColour has been added\r
*/\r
- public boolean hasMinColour()\r
- {\r
+ public boolean hasMinColour(\r
+ ) {\r
return this._has_minColour;\r
- } //-- boolean hasMinColour() \r
+ }\r
\r
/**\r
- * Method hasThreshold\r
- * \r
- * \r
+ * Method hasThreshold.\r
* \r
- * @return boolean\r
+ * @return true if at least one Threshold has been added\r
*/\r
- public boolean hasThreshold()\r
- {\r
+ public boolean hasThreshold(\r
+ ) {\r
return this._has_threshold;\r
- } //-- boolean hasThreshold() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'aboveThreshold'.\r
* \r
* @param aboveThreshold the value of field 'aboveThreshold'.\r
*/\r
- public void setAboveThreshold(int aboveThreshold)\r
- {\r
+ public void setAboveThreshold(\r
+ final int aboveThreshold) {\r
this._aboveThreshold = aboveThreshold;\r
this._has_aboveThreshold = true;\r
- } //-- void setAboveThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'annotation'.\r
* \r
* @param annotation the value of field 'annotation'.\r
*/\r
- public void setAnnotation(java.lang.String annotation)\r
- {\r
+ public void setAnnotation(\r
+ final java.lang.String annotation) {\r
this._annotation = annotation;\r
- } //-- void setAnnotation(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'colourScheme'.\r
* \r
* @param colourScheme the value of field 'colourScheme'.\r
*/\r
- public void setColourScheme(java.lang.String colourScheme)\r
- {\r
+ public void setColourScheme(\r
+ final java.lang.String colourScheme) {\r
this._colourScheme = colourScheme;\r
- } //-- void setColourScheme(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'maxColour'.\r
* \r
* @param maxColour the value of field 'maxColour'.\r
*/\r
- public void setMaxColour(int maxColour)\r
- {\r
+ public void setMaxColour(\r
+ final int maxColour) {\r
this._maxColour = maxColour;\r
this._has_maxColour = true;\r
- } //-- void setMaxColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'minColour'.\r
* \r
* @param minColour the value of field 'minColour'.\r
*/\r
- public void setMinColour(int minColour)\r
- {\r
+ public void setMinColour(\r
+ final int minColour) {\r
this._minColour = minColour;\r
this._has_minColour = true;\r
- } //-- void setMinColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'threshold'.\r
* \r
* @param threshold the value of field 'threshold'.\r
*/\r
- public void setThreshold(float threshold)\r
- {\r
+ public void setThreshold(\r
+ final float threshold) {\r
this._threshold = threshold;\r
this._has_threshold = true;\r
- } //-- void setThreshold(float) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.AnnotationColours\r
+ */\r
+ public static jalview.schemabinding.version2.AnnotationColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class AnnotationElement.\r
//--------------------------/\r
\r
/**\r
- * Field _position\r
+ * Field _position.\r
*/\r
private int _position;\r
\r
private boolean _has_position;\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private int _colour;\r
\r
private boolean _has_colour;\r
\r
/**\r
- * Field _displayCharacter\r
+ * Field _displayCharacter.\r
*/\r
private java.lang.String _displayCharacter;\r
\r
/**\r
- * Field _description\r
+ * Field _description.\r
*/\r
private java.lang.String _description;\r
\r
/**\r
- * Field _secondaryStructure\r
+ * Field _secondaryStructure.\r
*/\r
private java.lang.String _secondaryStructure;\r
\r
/**\r
- * Field _value\r
+ * Field _value.\r
*/\r
private float _value;\r
\r
\r
public AnnotationElement() {\r
super();\r
- } //-- jalview.schemabinding.version2.AnnotationElement()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteColour\r
- * \r
*/\r
- public void deleteColour()\r
- {\r
+ public void deleteColour(\r
+ ) {\r
this._has_colour= false;\r
- } //-- void deleteColour() \r
+ }\r
\r
/**\r
- * Method deletePosition\r
- * \r
*/\r
- public void deletePosition()\r
- {\r
+ public void deletePosition(\r
+ ) {\r
this._has_position= false;\r
- } //-- void deletePosition() \r
+ }\r
\r
/**\r
- * Method deleteValue\r
- * \r
*/\r
- public void deleteValue()\r
- {\r
+ public void deleteValue(\r
+ ) {\r
this._has_value= false;\r
- } //-- void deleteValue() \r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return int\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public int getColour()\r
- {\r
+ public int getColour(\r
+ ) {\r
return this._colour;\r
- } //-- int getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'description'.\r
* \r
- * @return String\r
- * @return the value of field 'description'.\r
+ * @return the value of field 'Description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription(\r
+ ) {\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ }\r
\r
/**\r
* Returns the value of field 'displayCharacter'.\r
* \r
- * @return String\r
- * @return the value of field 'displayCharacter'.\r
+ * @return the value of field 'DisplayCharacter'.\r
*/\r
- public java.lang.String getDisplayCharacter()\r
- {\r
+ public java.lang.String getDisplayCharacter(\r
+ ) {\r
return this._displayCharacter;\r
- } //-- java.lang.String getDisplayCharacter() \r
+ }\r
\r
/**\r
* Returns the value of field 'position'.\r
* \r
- * @return int\r
- * @return the value of field 'position'.\r
+ * @return the value of field 'Position'.\r
*/\r
- public int getPosition()\r
- {\r
+ public int getPosition(\r
+ ) {\r
return this._position;\r
- } //-- int getPosition() \r
+ }\r
\r
/**\r
* Returns the value of field 'secondaryStructure'.\r
* \r
- * @return String\r
- * @return the value of field 'secondaryStructure'.\r
+ * @return the value of field 'SecondaryStructure'.\r
*/\r
- public java.lang.String getSecondaryStructure()\r
- {\r
+ public java.lang.String getSecondaryStructure(\r
+ ) {\r
return this._secondaryStructure;\r
- } //-- java.lang.String getSecondaryStructure() \r
+ }\r
\r
/**\r
* Returns the value of field 'value'.\r
* \r
- * @return float\r
- * @return the value of field 'value'.\r
+ * @return the value of field 'Value'.\r
*/\r
- public float getValue()\r
- {\r
+ public float getValue(\r
+ ) {\r
return this._value;\r
- } //-- float getValue() \r
+ }\r
\r
/**\r
- * Method hasColour\r
- * \r
- * \r
+ * Method hasColour.\r
* \r
- * @return boolean\r
+ * @return true if at least one Colour has been added\r
*/\r
- public boolean hasColour()\r
- {\r
+ public boolean hasColour(\r
+ ) {\r
return this._has_colour;\r
- } //-- boolean hasColour() \r
+ }\r
\r
/**\r
- * Method hasPosition\r
+ * Method hasPosition.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Position has been added\r
*/\r
- public boolean hasPosition()\r
- {\r
+ public boolean hasPosition(\r
+ ) {\r
return this._has_position;\r
- } //-- boolean hasPosition() \r
+ }\r
\r
/**\r
- * Method hasValue\r
- * \r
+ * Method hasValue.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Value has been added\r
*/\r
- public boolean hasValue()\r
- {\r
+ public boolean hasValue(\r
+ ) {\r
return this._has_value;\r
- } //-- boolean hasValue() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(int colour)\r
- {\r
+ public void setColour(\r
+ final int colour) {\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'description'.\r
* \r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'displayCharacter'.\r
* \r
* @param displayCharacter the value of field 'displayCharacter'\r
*/\r
- public void setDisplayCharacter(java.lang.String displayCharacter)\r
- {\r
+ public void setDisplayCharacter(\r
+ final java.lang.String displayCharacter) {\r
this._displayCharacter = displayCharacter;\r
- } //-- void setDisplayCharacter(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'position'.\r
* \r
* @param position the value of field 'position'.\r
*/\r
- public void setPosition(int position)\r
- {\r
+ public void setPosition(\r
+ final int position) {\r
this._position = position;\r
this._has_position = true;\r
- } //-- void setPosition(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'secondaryStructure'.\r
* @param secondaryStructure the value of field\r
* 'secondaryStructure'.\r
*/\r
- public void setSecondaryStructure(java.lang.String secondaryStructure)\r
- {\r
+ public void setSecondaryStructure(\r
+ final java.lang.String secondaryStructure) {\r
this._secondaryStructure = secondaryStructure;\r
- } //-- void setSecondaryStructure(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'value'.\r
* \r
* @param value the value of field 'value'.\r
*/\r
- public void setValue(float value)\r
- {\r
+ public void setValue(\r
+ final float value) {\r
this._value = value;\r
this._has_value = true;\r
- } //-- void setValue(float) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.AnnotationElement\r
+ */\r
+ public static jalview.schemabinding.version2.AnnotationElement unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Colour.\r
//--------------------------/\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
/**\r
- * Field _RGB\r
+ * Field _RGB.\r
*/\r
private java.lang.String _RGB;\r
\r
\r
public Colour() {\r
super();\r
- } //-- jalview.schemabinding.version2.Colour()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'name'.\r
* \r
- * @return String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
* Returns the value of field 'RGB'.\r
* \r
- * @return String\r
* @return the value of field 'RGB'.\r
*/\r
- public java.lang.String getRGB()\r
- {\r
+ public java.lang.String getRGB(\r
+ ) {\r
return this._RGB;\r
- } //-- java.lang.String getRGB() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'RGB'.\r
* \r
* @param RGB the value of field 'RGB'.\r
*/\r
- public void setRGB(java.lang.String RGB)\r
- {\r
+ public void setRGB(\r
+ final java.lang.String RGB) {\r
this._RGB = RGB;\r
- } //-- void setRGB(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Colour\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.Colour unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class DBRef.\r
//--------------------------/\r
\r
/**\r
- * Field _source\r
+ * Field _source.\r
*/\r
private java.lang.String _source;\r
\r
/**\r
- * Field _version\r
+ * Field _version.\r
*/\r
private java.lang.String _version;\r
\r
/**\r
- * Field _accessionId\r
+ * Field _accessionId.\r
*/\r
private java.lang.String _accessionId;\r
\r
\r
public DBRef() {\r
super();\r
- } //-- jalview.schemabinding.version2.DBRef()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'accessionId'.\r
* \r
- * @return String\r
- * @return the value of field 'accessionId'.\r
+ * @return the value of field 'AccessionId'.\r
*/\r
- public java.lang.String getAccessionId()\r
- {\r
+ public java.lang.String getAccessionId(\r
+ ) {\r
return this._accessionId;\r
- } //-- java.lang.String getAccessionId() \r
+ }\r
\r
/**\r
* Returns the value of field 'source'.\r
* \r
- * @return String\r
- * @return the value of field 'source'.\r
+ * @return the value of field 'Source'.\r
*/\r
- public java.lang.String getSource()\r
- {\r
+ public java.lang.String getSource(\r
+ ) {\r
return this._source;\r
- } //-- java.lang.String getSource() \r
+ }\r
\r
/**\r
* Returns the value of field 'version'.\r
* \r
- * @return String\r
- * @return the value of field 'version'.\r
+ * @return the value of field 'Version'.\r
*/\r
- public java.lang.String getVersion()\r
- {\r
+ public java.lang.String getVersion(\r
+ ) {\r
return this._version;\r
- } //-- java.lang.String getVersion() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'accessionId'.\r
* \r
* @param accessionId the value of field 'accessionId'.\r
*/\r
- public void setAccessionId(java.lang.String accessionId)\r
- {\r
+ public void setAccessionId(\r
+ final java.lang.String accessionId) {\r
this._accessionId = accessionId;\r
- } //-- void setAccessionId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'source'.\r
* \r
* @param source the value of field 'source'.\r
*/\r
- public void setSource(java.lang.String source)\r
- {\r
+ public void setSource(\r
+ final java.lang.String source) {\r
this._source = source;\r
- } //-- void setSource(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'version'.\r
* \r
* @param version the value of field 'version'.\r
*/\r
- public void setVersion(java.lang.String version)\r
- {\r
+ public void setVersion(\r
+ final java.lang.String version) {\r
this._version = version;\r
- } //-- void setVersion(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.DBRef\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.DBRef unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Feature.\r
//--------------------------/\r
\r
/**\r
- * Field _begin\r
+ * Field _begin.\r
*/\r
private int _begin;\r
\r
private boolean _has_begin;\r
\r
/**\r
- * Field _end\r
+ * Field _end.\r
*/\r
private int _end;\r
\r
private boolean _has_end;\r
\r
/**\r
- * Field _type\r
+ * Field _type.\r
*/\r
private java.lang.String _type;\r
\r
/**\r
- * Field _description\r
+ * Field _description.\r
*/\r
private java.lang.String _description;\r
\r
/**\r
- * Field _status\r
+ * Field _status.\r
*/\r
private java.lang.String _status;\r
\r
/**\r
- * Field _featureGroup\r
+ * Field _featureGroup.\r
*/\r
private java.lang.String _featureGroup;\r
\r
/**\r
- * Field _score\r
+ * Field _score.\r
*/\r
private float _score;\r
\r
private boolean _has_score;\r
\r
/**\r
- * Field _otherDataList\r
+ * Field _otherDataList.\r
*/\r
private java.util.Vector _otherDataList;\r
\r
\r
public Feature() {\r
super();\r
- _otherDataList = new Vector();\r
- } //-- jalview.schemabinding.version2.Feature()\r
+ this._otherDataList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addOtherData\r
- * \r
* \r
* \r
* @param vOtherData\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _otherDataList.addElement(vOtherData);\r
- } //-- void addOtherData(jalview.schemabinding.version2.OtherData) \r
+ public void addOtherData(\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._otherDataList.addElement(vOtherData);\r
+ }\r
\r
/**\r
- * Method addOtherData\r
- * \r
* \r
* \r
* @param index\r
* @param vOtherData\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _otherDataList.insertElementAt(vOtherData, index);\r
- } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) \r
+ public void addOtherData(\r
+ final int index,\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._otherDataList.add(index, vOtherData);\r
+ }\r
\r
/**\r
- * Method deleteBegin\r
- * \r
*/\r
- public void deleteBegin()\r
- {\r
+ public void deleteBegin(\r
+ ) {\r
this._has_begin= false;\r
- } //-- void deleteBegin() \r
+ }\r
\r
/**\r
- * Method deleteEnd\r
- * \r
*/\r
- public void deleteEnd()\r
- {\r
+ public void deleteEnd(\r
+ ) {\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ }\r
\r
/**\r
- * Method deleteScore\r
- * \r
*/\r
- public void deleteScore()\r
- {\r
+ public void deleteScore(\r
+ ) {\r
this._has_score= false;\r
- } //-- void deleteScore() \r
+ }\r
\r
/**\r
- * Method enumerateOtherData\r
- * \r
+ * Method enumerateOtherData.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.OtherData elements\r
*/\r
- public java.util.Enumeration enumerateOtherData()\r
- {\r
- return _otherDataList.elements();\r
- } //-- java.util.Enumeration enumerateOtherData() \r
+ public java.util.Enumeration enumerateOtherData(\r
+ ) {\r
+ return this._otherDataList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'begin'.\r
* \r
- * @return int\r
- * @return the value of field 'begin'.\r
+ * @return the value of field 'Begin'.\r
*/\r
- public int getBegin()\r
- {\r
+ public int getBegin(\r
+ ) {\r
return this._begin;\r
- } //-- int getBegin() \r
+ }\r
\r
/**\r
* Returns the value of field 'description'.\r
* \r
- * @return String\r
- * @return the value of field 'description'.\r
+ * @return the value of field 'Description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription(\r
+ ) {\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ }\r
\r
/**\r
* Returns the value of field 'end'.\r
* \r
- * @return int\r
- * @return the value of field 'end'.\r
+ * @return the value of field 'End'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd(\r
+ ) {\r
return this._end;\r
- } //-- int getEnd() \r
+ }\r
\r
/**\r
* Returns the value of field 'featureGroup'.\r
* \r
- * @return String\r
- * @return the value of field 'featureGroup'.\r
+ * @return the value of field 'FeatureGroup'.\r
*/\r
- public java.lang.String getFeatureGroup()\r
- {\r
+ public java.lang.String getFeatureGroup(\r
+ ) {\r
return this._featureGroup;\r
- } //-- java.lang.String getFeatureGroup() \r
+ }\r
\r
/**\r
- * Method getOtherData\r
- * \r
- * \r
+ * Method getOtherData.\r
* \r
* @param index\r
- * @return OtherData\r
- */\r
- public jalview.schemabinding.version2.OtherData getOtherData(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _otherDataList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.OtherData at the given index\r
+ */\r
+ public jalview.schemabinding.version2.OtherData getOtherData(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._otherDataList.size()) {\r
+ throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.OtherData getOtherData(int) \r
+ return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);\r
+ }\r
\r
/**\r
- * Method getOtherData\r
- * \r
- * \r
+ * Method getOtherData.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return OtherData\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.OtherData[] getOtherData()\r
- {\r
- int size = _otherDataList.size();\r
- jalview.schemabinding.version2.OtherData[] mArray = new jalview.schemabinding.version2.OtherData[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.OtherData[] getOtherData() \r
+ public jalview.schemabinding.version2.OtherData[] getOtherData(\r
+ ) {\r
+ jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];\r
+ return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getOtherDataCount\r
- * \r
- * \r
+ * Method getOtherDataCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getOtherDataCount()\r
- {\r
- return _otherDataList.size();\r
- } //-- int getOtherDataCount() \r
+ public int getOtherDataCount(\r
+ ) {\r
+ return this._otherDataList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'score'.\r
* \r
- * @return float\r
- * @return the value of field 'score'.\r
+ * @return the value of field 'Score'.\r
*/\r
- public float getScore()\r
- {\r
+ public float getScore(\r
+ ) {\r
return this._score;\r
- } //-- float getScore() \r
+ }\r
\r
/**\r
* Returns the value of field 'status'.\r
* \r
- * @return String\r
- * @return the value of field 'status'.\r
+ * @return the value of field 'Status'.\r
*/\r
- public java.lang.String getStatus()\r
- {\r
+ public java.lang.String getStatus(\r
+ ) {\r
return this._status;\r
- } //-- java.lang.String getStatus() \r
+ }\r
\r
/**\r
* Returns the value of field 'type'.\r
* \r
- * @return String\r
- * @return the value of field 'type'.\r
+ * @return the value of field 'Type'.\r
*/\r
- public java.lang.String getType()\r
- {\r
+ public java.lang.String getType(\r
+ ) {\r
return this._type;\r
- } //-- java.lang.String getType() \r
+ }\r
\r
/**\r
- * Method hasBegin\r
+ * Method hasBegin.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Begin has been added\r
*/\r
- public boolean hasBegin()\r
- {\r
+ public boolean hasBegin(\r
+ ) {\r
return this._has_begin;\r
- } //-- boolean hasBegin() \r
+ }\r
\r
/**\r
- * Method hasEnd\r
- * \r
+ * Method hasEnd.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one End has been added\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd(\r
+ ) {\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ }\r
\r
/**\r
- * Method hasScore\r
- * \r
- * \r
+ * Method hasScore.\r
* \r
- * @return boolean\r
+ * @return true if at least one Score has been added\r
*/\r
- public boolean hasScore()\r
- {\r
+ public boolean hasScore(\r
+ ) {\r
return this._has_score;\r
- } //-- boolean hasScore() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
- * \r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllOtherData\r
- * \r
*/\r
- public void removeAllOtherData()\r
- {\r
- _otherDataList.removeAllElements();\r
- } //-- void removeAllOtherData() \r
+ public void removeAllOtherData(\r
+ ) {\r
+ this._otherDataList.clear();\r
+ }\r
\r
/**\r
- * Method removeOtherData\r
- * \r
+ * Method removeOtherData.\r
* \r
+ * @param vOtherData\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeOtherData(\r
+ final jalview.schemabinding.version2.OtherData vOtherData) {\r
+ boolean removed = _otherDataList.remove(vOtherData);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeOtherDataAt.\r
* \r
* @param index\r
- * @return OtherData\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.OtherData removeOtherData(int index)\r
- {\r
- java.lang.Object obj = _otherDataList.elementAt(index);\r
- _otherDataList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.OtherData removeOtherDataAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._otherDataList.remove(index);\r
return (jalview.schemabinding.version2.OtherData) obj;\r
- } //-- jalview.schemabinding.version2.OtherData removeOtherData(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'begin'.\r
* \r
* @param begin the value of field 'begin'.\r
*/\r
- public void setBegin(int begin)\r
- {\r
+ public void setBegin(\r
+ final int begin) {\r
this._begin = begin;\r
this._has_begin = true;\r
- } //-- void setBegin(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'description'.\r
* \r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'end'.\r
* \r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(\r
+ final int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'featureGroup'.\r
* \r
* @param featureGroup the value of field 'featureGroup'.\r
*/\r
- public void setFeatureGroup(java.lang.String featureGroup)\r
- {\r
+ public void setFeatureGroup(\r
+ final java.lang.String featureGroup) {\r
this._featureGroup = featureGroup;\r
- } //-- void setFeatureGroup(java.lang.String) \r
+ }\r
\r
/**\r
- * Method setOtherData\r
- * \r
* \r
* \r
* @param index\r
* @param vOtherData\r
- */\r
- public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _otherDataList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setOtherData(\r
+ final int index,\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._otherDataList.size()) {\r
+ throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");\r
}\r
- _otherDataList.setElementAt(vOtherData, index);\r
- } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData) \r
+ \r
+ this._otherDataList.set(index, vOtherData);\r
+ }\r
\r
/**\r
- * Method setOtherData\r
- * \r
* \r
* \r
- * @param otherDataArray\r
+ * @param vOtherDataArray\r
*/\r
- public void setOtherData(jalview.schemabinding.version2.OtherData[] otherDataArray)\r
- {\r
+ public void setOtherData(\r
+ final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {\r
//-- copy array\r
- _otherDataList.removeAllElements();\r
- for (int i = 0; i < otherDataArray.length; i++) {\r
- _otherDataList.addElement(otherDataArray[i]);\r
+ _otherDataList.clear();\r
+ \r
+ for (int i = 0; i < vOtherDataArray.length; i++) {\r
+ this._otherDataList.add(vOtherDataArray[i]);\r
}\r
- } //-- void setOtherData(jalview.schemabinding.version2.OtherData) \r
+ }\r
\r
/**\r
* Sets the value of field 'score'.\r
* \r
* @param score the value of field 'score'.\r
*/\r
- public void setScore(float score)\r
- {\r
+ public void setScore(\r
+ final float score) {\r
this._score = score;\r
this._has_score = true;\r
- } //-- void setScore(float) \r
+ }\r
\r
/**\r
* Sets the value of field 'status'.\r
* \r
* @param status the value of field 'status'.\r
*/\r
- public void setStatus(java.lang.String status)\r
- {\r
+ public void setStatus(\r
+ final java.lang.String status) {\r
this._status = status;\r
- } //-- void setStatus(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'type'.\r
* \r
* @param type the value of field 'type'.\r
*/\r
- public void setType(java.lang.String type)\r
- {\r
+ public void setType(\r
+ final java.lang.String type) {\r
this._type = type;\r
- } //-- void setType(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Featur\r
+ */\r
+ public static jalview.schemabinding.version2.Feature unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class FeatureSettings.\r
//--------------------------/\r
\r
/**\r
- * Field _settingList\r
+ * Field _settingList.\r
*/\r
private java.util.Vector _settingList;\r
\r
/**\r
- * Field _groupList\r
+ * Field _groupList.\r
*/\r
private java.util.Vector _groupList;\r
\r
\r
public FeatureSettings() {\r
super();\r
- _settingList = new Vector();\r
- _groupList = new Vector();\r
- } //-- jalview.schemabinding.version2.FeatureSettings()\r
+ this._settingList = new java.util.Vector();\r
+ this._groupList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addGroup\r
- * \r
* \r
* \r
* @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addGroup(jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _groupList.addElement(vGroup);\r
- } //-- void addGroup(jalview.schemabinding.version2.Group) \r
+ public void addGroup(\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._groupList.addElement(vGroup);\r
+ }\r
\r
/**\r
- * Method addGroup\r
- * \r
* \r
* \r
* @param index\r
* @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addGroup(int index, jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _groupList.insertElementAt(vGroup, index);\r
- } //-- void addGroup(int, jalview.schemabinding.version2.Group) \r
+ public void addGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._groupList.add(index, vGroup);\r
+ }\r
\r
/**\r
- * Method addSetting\r
- * \r
* \r
* \r
* @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSetting(jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _settingList.addElement(vSetting);\r
- } //-- void addSetting(jalview.schemabinding.version2.Setting) \r
+ public void addSetting(\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._settingList.addElement(vSetting);\r
+ }\r
\r
/**\r
- * Method addSetting\r
- * \r
* \r
* \r
* @param index\r
* @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSetting(int index, jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _settingList.insertElementAt(vSetting, index);\r
- } //-- void addSetting(int, jalview.schemabinding.version2.Setting) \r
+ public void addSetting(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._settingList.add(index, vSetting);\r
+ }\r
\r
/**\r
- * Method enumerateGroup\r
+ * Method enumerateGroup.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Group elements\r
*/\r
- public java.util.Enumeration enumerateGroup()\r
- {\r
- return _groupList.elements();\r
- } //-- java.util.Enumeration enumerateGroup() \r
+ public java.util.Enumeration enumerateGroup(\r
+ ) {\r
+ return this._groupList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateSetting\r
- * \r
+ * Method enumerateSetting.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Setting elements\r
*/\r
- public java.util.Enumeration enumerateSetting()\r
- {\r
- return _settingList.elements();\r
- } //-- java.util.Enumeration enumerateSetting() \r
+ public java.util.Enumeration enumerateSetting(\r
+ ) {\r
+ return this._settingList.elements();\r
+ }\r
\r
/**\r
- * Method getGroup\r
- * \r
- * \r
+ * Method getGroup.\r
* \r
* @param index\r
- * @return Group\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Group at the given index\r
*/\r
- public jalview.schemabinding.version2.Group getGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _groupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.Group getGroup(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._groupList.size()) {\r
+ throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Group) _groupList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Group getGroup(int) \r
+ return (jalview.schemabinding.version2.Group) _groupList.get(index);\r
+ }\r
\r
/**\r
- * Method getGroup\r
+ * Method getGroup.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return Group\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Group[] getGroup()\r
- {\r
- int size = _groupList.size();\r
- jalview.schemabinding.version2.Group[] mArray = new jalview.schemabinding.version2.Group[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Group) _groupList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Group[] getGroup() \r
+ public jalview.schemabinding.version2.Group[] getGroup(\r
+ ) {\r
+ jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];\r
+ return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getGroupCount\r
+ * Method getGroupCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getGroupCount()\r
- {\r
- return _groupList.size();\r
- } //-- int getGroupCount() \r
+ public int getGroupCount(\r
+ ) {\r
+ return this._groupList.size();\r
+ }\r
\r
/**\r
- * Method getSetting\r
- * \r
- * \r
+ * Method getSetting.\r
* \r
* @param index\r
- * @return Setting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Setting at the given index\r
*/\r
- public jalview.schemabinding.version2.Setting getSetting(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _settingList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.Setting getSetting(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._settingList.size()) {\r
+ throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Setting getSetting(int) \r
+ return (jalview.schemabinding.version2.Setting) _settingList.get(index);\r
+ }\r
\r
/**\r
- * Method getSetting\r
+ * Method getSetting.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return Setting\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Setting[] getSetting()\r
- {\r
- int size = _settingList.size();\r
- jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.version2.Setting[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Setting[] getSetting() \r
+ public jalview.schemabinding.version2.Setting[] getSetting(\r
+ ) {\r
+ jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];\r
+ return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getSettingCount\r
+ * Method getSettingCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSettingCount()\r
- {\r
- return _settingList.size();\r
- } //-- int getSettingCount() \r
+ public int getSettingCount(\r
+ ) {\r
+ return this._settingList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllGroup\r
- * \r
*/\r
- public void removeAllGroup()\r
- {\r
- _groupList.removeAllElements();\r
- } //-- void removeAllGroup() \r
+ public void removeAllGroup(\r
+ ) {\r
+ this._groupList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllSetting\r
- * \r
*/\r
- public void removeAllSetting()\r
- {\r
- _settingList.removeAllElements();\r
- } //-- void removeAllSetting() \r
+ public void removeAllSetting(\r
+ ) {\r
+ this._settingList.clear();\r
+ }\r
\r
/**\r
- * Method removeGroup\r
- * \r
+ * Method removeGroup.\r
* \r
+ * @param vGroup\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeGroup(\r
+ final jalview.schemabinding.version2.Group vGroup) {\r
+ boolean removed = _groupList.remove(vGroup);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeGroupAt.\r
* \r
* @param index\r
- * @return Group\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Group removeGroup(int index)\r
- {\r
- java.lang.Object obj = _groupList.elementAt(index);\r
- _groupList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Group removeGroupAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._groupList.remove(index);\r
return (jalview.schemabinding.version2.Group) obj;\r
- } //-- jalview.schemabinding.version2.Group removeGroup(int) \r
+ }\r
\r
/**\r
- * Method removeSetting\r
- * \r
+ * Method removeSetting.\r
* \r
+ * @param vSetting\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSetting(\r
+ final jalview.schemabinding.version2.Setting vSetting) {\r
+ boolean removed = _settingList.remove(vSetting);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSettingAt.\r
* \r
* @param index\r
- * @return Setting\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Setting removeSetting(int index)\r
- {\r
- java.lang.Object obj = _settingList.elementAt(index);\r
- _settingList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Setting removeSettingAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._settingList.remove(index);\r
return (jalview.schemabinding.version2.Setting) obj;\r
- } //-- jalview.schemabinding.version2.Setting removeSetting(int) \r
+ }\r
\r
/**\r
- * Method setGroup\r
- * \r
* \r
* \r
* @param index\r
* @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setGroup(int index, jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _groupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._groupList.size()) {\r
+ throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
}\r
- _groupList.setElementAt(vGroup, index);\r
- } //-- void setGroup(int, jalview.schemabinding.version2.Group) \r
+ \r
+ this._groupList.set(index, vGroup);\r
+ }\r
\r
/**\r
- * Method setGroup\r
* \r
* \r
- * \r
- * @param groupArray\r
+ * @param vGroupArray\r
*/\r
- public void setGroup(jalview.schemabinding.version2.Group[] groupArray)\r
- {\r
+ public void setGroup(\r
+ final jalview.schemabinding.version2.Group[] vGroupArray) {\r
//-- copy array\r
- _groupList.removeAllElements();\r
- for (int i = 0; i < groupArray.length; i++) {\r
- _groupList.addElement(groupArray[i]);\r
+ _groupList.clear();\r
+ \r
+ for (int i = 0; i < vGroupArray.length; i++) {\r
+ this._groupList.add(vGroupArray[i]);\r
}\r
- } //-- void setGroup(jalview.schemabinding.version2.Group) \r
+ }\r
\r
/**\r
- * Method setSetting\r
- * \r
* \r
* \r
* @param index\r
* @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setSetting(int index, jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _settingList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setSetting(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._settingList.size()) {\r
+ throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");\r
}\r
- _settingList.setElementAt(vSetting, index);\r
- } //-- void setSetting(int, jalview.schemabinding.version2.Setting) \r
+ \r
+ this._settingList.set(index, vSetting);\r
+ }\r
\r
/**\r
- * Method setSetting\r
- * \r
* \r
* \r
- * @param settingArray\r
+ * @param vSettingArray\r
*/\r
- public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)\r
- {\r
+ public void setSetting(\r
+ final jalview.schemabinding.version2.Setting[] vSettingArray) {\r
//-- copy array\r
- _settingList.removeAllElements();\r
- for (int i = 0; i < settingArray.length; i++) {\r
- _settingList.addElement(settingArray[i]);\r
+ _settingList.clear();\r
+ \r
+ for (int i = 0; i < vSettingArray.length; i++) {\r
+ this._settingList.add(vSettingArray[i]);\r
}\r
- } //-- void setSetting(jalview.schemabinding.version2.Setting) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.FeatureSettings\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.FeatureSettings unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Features.\r
\r
public Features() {\r
super();\r
- } //-- jalview.schemabinding.version2.Features()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Featur\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ public static jalview.schemabinding.version2.Feature unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Group.\r
//--------------------------/\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
/**\r
- * Field _display\r
+ * Field _display.\r
*/\r
private boolean _display;\r
\r
\r
public Group() {\r
super();\r
- } //-- jalview.schemabinding.version2.Group()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteDisplay\r
- * \r
*/\r
- public void deleteDisplay()\r
- {\r
+ public void deleteDisplay(\r
+ ) {\r
this._has_display= false;\r
- } //-- void deleteDisplay() \r
+ }\r
\r
/**\r
* Returns the value of field 'display'.\r
* \r
- * @return boolean\r
- * @return the value of field 'display'.\r
+ * @return the value of field 'Display'.\r
*/\r
- public boolean getDisplay()\r
- {\r
+ public boolean getDisplay(\r
+ ) {\r
return this._display;\r
- } //-- boolean getDisplay() \r
+ }\r
\r
/**\r
* Returns the value of field 'name'.\r
* \r
- * @return String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
- * Method hasDisplay\r
- * \r
+ * Method hasDisplay.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Display has been added\r
*/\r
- public boolean hasDisplay()\r
- {\r
+ public boolean hasDisplay(\r
+ ) {\r
return this._has_display;\r
- } //-- boolean hasDisplay() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Returns the value of field 'display'.\r
* \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean isDisplay(\r
+ ) {\r
+ return this._display;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'display'.\r
* \r
* @param display the value of field 'display'.\r
*/\r
- public void setDisplay(boolean display)\r
- {\r
+ public void setDisplay(\r
+ final boolean display) {\r
this._display = display;\r
this._has_display = true;\r
- } //-- void setDisplay(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Group\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.Group unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class HiddenColumns.\r
//--------------------------/\r
\r
/**\r
- * Field _start\r
+ * Field _start.\r
*/\r
private int _start;\r
\r
private boolean _has_start;\r
\r
/**\r
- * Field _end\r
+ * Field _end.\r
*/\r
private int _end;\r
\r
\r
public HiddenColumns() {\r
super();\r
- } //-- jalview.schemabinding.version2.HiddenColumns()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteEnd\r
- * \r
*/\r
- public void deleteEnd()\r
- {\r
+ public void deleteEnd(\r
+ ) {\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ }\r
\r
/**\r
- * Method deleteStart\r
- * \r
*/\r
- public void deleteStart()\r
- {\r
+ public void deleteStart(\r
+ ) {\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ }\r
\r
/**\r
* Returns the value of field 'end'.\r
* \r
- * @return int\r
- * @return the value of field 'end'.\r
+ * @return the value of field 'End'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd(\r
+ ) {\r
return this._end;\r
- } //-- int getEnd() \r
+ }\r
\r
/**\r
* Returns the value of field 'start'.\r
* \r
- * @return int\r
- * @return the value of field 'start'.\r
+ * @return the value of field 'Start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart(\r
+ ) {\r
return this._start;\r
- } //-- int getStart() \r
+ }\r
\r
/**\r
- * Method hasEnd\r
- * \r
+ * Method hasEnd.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one End has been added\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd(\r
+ ) {\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ }\r
\r
/**\r
- * Method hasStart\r
- * \r
+ * Method hasStart.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Start has been added\r
*/\r
- public boolean hasStart()\r
- {\r
+ public boolean hasStart(\r
+ ) {\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'end'.\r
* \r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(\r
+ final int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'start'.\r
* \r
* @param start the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(\r
+ final int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.HiddenColumns\r
+ */\r
+ public static jalview.schemabinding.version2.HiddenColumns unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JGroup.\r
//--------------------------/\r
\r
/**\r
- * Field _start\r
+ * Field _start.\r
*/\r
private int _start;\r
\r
private boolean _has_start;\r
\r
/**\r
- * Field _end\r
+ * Field _end.\r
*/\r
private int _end;\r
\r
private boolean _has_end;\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private java.lang.String _colour;\r
\r
/**\r
- * Field _consThreshold\r
+ * Field _consThreshold.\r
*/\r
private int _consThreshold;\r
\r
private boolean _has_consThreshold;\r
\r
/**\r
- * Field _pidThreshold\r
+ * Field _pidThreshold.\r
*/\r
private int _pidThreshold;\r
\r
private boolean _has_pidThreshold;\r
\r
/**\r
- * Field _outlineColour\r
+ * Field _outlineColour.\r
*/\r
private int _outlineColour;\r
\r
private boolean _has_outlineColour;\r
\r
/**\r
- * Field _displayBoxes\r
+ * Field _displayBoxes.\r
*/\r
private boolean _displayBoxes;\r
\r
private boolean _has_displayBoxes;\r
\r
/**\r
- * Field _displayText\r
+ * Field _displayText.\r
*/\r
private boolean _displayText;\r
\r
private boolean _has_displayText;\r
\r
/**\r
- * Field _colourText\r
+ * Field _colourText.\r
*/\r
private boolean _colourText;\r
\r
private boolean _has_colourText;\r
\r
/**\r
- * Field _textCol1\r
+ * Field _textCol1.\r
*/\r
private int _textCol1;\r
\r
private boolean _has_textCol1;\r
\r
/**\r
- * Field _textCol2\r
+ * Field _textCol2.\r
*/\r
private int _textCol2;\r
\r
private boolean _has_textCol2;\r
\r
/**\r
- * Field _textColThreshold\r
+ * Field _textColThreshold.\r
*/\r
private int _textColThreshold;\r
\r
private boolean _has_textColThreshold;\r
\r
/**\r
- * Field _seqList\r
+ * Field _seqList.\r
*/\r
private java.util.Vector _seqList;\r
\r
\r
public JGroup() {\r
super();\r
- _seqList = new Vector();\r
- } //-- jalview.schemabinding.version2.JGroup()\r
+ this._seqList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addSeq\r
- * \r
* \r
* \r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSeq(int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int) \r
+ public void addSeq(\r
+ final int vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.addElement(new java.lang.Integer(vSeq));\r
+ }\r
\r
/**\r
- * Method addSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int) \r
+ public void addSeq(\r
+ final int index,\r
+ final int vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.add(index, new java.lang.Integer(vSeq));\r
+ }\r
\r
/**\r
- * Method deleteColourText\r
- * \r
*/\r
- public void deleteColourText()\r
- {\r
+ public void deleteColourText(\r
+ ) {\r
this._has_colourText= false;\r
- } //-- void deleteColourText() \r
+ }\r
\r
/**\r
- * Method deleteConsThreshold\r
- * \r
*/\r
- public void deleteConsThreshold()\r
- {\r
+ public void deleteConsThreshold(\r
+ ) {\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ }\r
\r
/**\r
- * Method deleteDisplayBoxes\r
- * \r
*/\r
- public void deleteDisplayBoxes()\r
- {\r
+ public void deleteDisplayBoxes(\r
+ ) {\r
this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes() \r
+ }\r
\r
/**\r
- * Method deleteDisplayText\r
- * \r
*/\r
- public void deleteDisplayText()\r
- {\r
+ public void deleteDisplayText(\r
+ ) {\r
this._has_displayText= false;\r
- } //-- void deleteDisplayText() \r
+ }\r
\r
/**\r
- * Method deleteEnd\r
- * \r
*/\r
- public void deleteEnd()\r
- {\r
+ public void deleteEnd(\r
+ ) {\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ }\r
\r
/**\r
- * Method deleteOutlineColour\r
- * \r
*/\r
- public void deleteOutlineColour()\r
- {\r
+ public void deleteOutlineColour(\r
+ ) {\r
this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour() \r
+ }\r
\r
/**\r
- * Method deletePidThreshold\r
- * \r
*/\r
- public void deletePidThreshold()\r
- {\r
+ public void deletePidThreshold(\r
+ ) {\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ }\r
\r
/**\r
- * Method deleteStart\r
- * \r
*/\r
- public void deleteStart()\r
- {\r
+ public void deleteStart(\r
+ ) {\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ }\r
\r
/**\r
- * Method deleteTextCol1\r
- * \r
*/\r
- public void deleteTextCol1()\r
- {\r
+ public void deleteTextCol1(\r
+ ) {\r
this._has_textCol1= false;\r
- } //-- void deleteTextCol1() \r
+ }\r
\r
/**\r
- * Method deleteTextCol2\r
- * \r
*/\r
- public void deleteTextCol2()\r
- {\r
+ public void deleteTextCol2(\r
+ ) {\r
this._has_textCol2= false;\r
- } //-- void deleteTextCol2() \r
+ }\r
\r
/**\r
- * Method deleteTextColThreshold\r
- * \r
*/\r
- public void deleteTextColThreshold()\r
- {\r
+ public void deleteTextColThreshold(\r
+ ) {\r
this._has_textColThreshold= false;\r
- } //-- void deleteTextColThreshold() \r
+ }\r
\r
/**\r
- * Method enumerateSeq\r
- * \r
+ * Method enumerateSeq.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all int elements\r
*/\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
- return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq() \r
+ public java.util.Enumeration enumerateSeq(\r
+ ) {\r
+ return this._seqList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return String\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public java.lang.String getColour()\r
- {\r
+ public java.lang.String getColour(\r
+ ) {\r
return this._colour;\r
- } //-- java.lang.String getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'colourText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'colourText'.\r
+ * @return the value of field 'ColourText'.\r
*/\r
- public boolean getColourText()\r
- {\r
+ public boolean getColourText(\r
+ ) {\r
return this._colourText;\r
- } //-- boolean getColourText() \r
+ }\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
+ * @return the value of field 'ConsThreshold'.\r
*/\r
- public int getConsThreshold()\r
- {\r
+ public int getConsThreshold(\r
+ ) {\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
* \r
- * @return boolean\r
- * @return the value of field 'displayBoxes'.\r
+ * @return the value of field 'DisplayBoxes'.\r
*/\r
- public boolean getDisplayBoxes()\r
- {\r
+ public boolean getDisplayBoxes(\r
+ ) {\r
return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes() \r
+ }\r
\r
/**\r
* Returns the value of field 'displayText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'displayText'.\r
+ * @return the value of field 'DisplayText'.\r
*/\r
- public boolean getDisplayText()\r
- {\r
+ public boolean getDisplayText(\r
+ ) {\r
return this._displayText;\r
- } //-- boolean getDisplayText() \r
+ }\r
\r
/**\r
* Returns the value of field 'end'.\r
* \r
- * @return int\r
- * @return the value of field 'end'.\r
+ * @return the value of field 'End'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd(\r
+ ) {\r
return this._end;\r
- } //-- int getEnd() \r
+ }\r
\r
/**\r
* Returns the value of field 'name'.\r
* \r
- * @return String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
* \r
- * @return int\r
- * @return the value of field 'outlineColour'.\r
+ * @return the value of field 'OutlineColour'.\r
*/\r
- public int getOutlineColour()\r
- {\r
+ public int getOutlineColour(\r
+ ) {\r
return this._outlineColour;\r
- } //-- int getOutlineColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
+ * @return the value of field 'PidThreshold'.\r
*/\r
- public int getPidThreshold()\r
- {\r
+ public int getPidThreshold(\r
+ ) {\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ }\r
\r
/**\r
- * Method getSeq\r
- * \r
- * \r
+ * Method getSeq.\r
* \r
* @param index\r
- * @return int\r
- */\r
- public int getSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the int at the given index\r
+ */\r
+ public int getSeq(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size()) {\r
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
}\r
\r
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int) \r
+ return ((java.lang.Integer) _seqList.get(index)).intValue();\r
+ }\r
\r
/**\r
- * Method getSeq\r
- * \r
- * \r
+ * Method getSeq.Returns the contents of the collection in an\r
+ * Array. \r
* \r
- * @return int\r
+ * @return this collection as an Array\r
*/\r
- public int[] getSeq()\r
- {\r
- int size = _seqList.size();\r
- int[] mArray = new int[size];\r
+ public int[] getSeq(\r
+ ) {\r
+ int size = this._seqList.size();\r
+ int[] array = new int[size];\r
+ java.util.Iterator iter = _seqList.iterator();\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+ array[index] = ((java.lang.Integer) iter.next()).intValue();\r
}\r
- return mArray;\r
- } //-- int[] getSeq() \r
+ return array;\r
+ }\r
\r
/**\r
- * Method getSeqCount\r
- * \r
- * \r
+ * Method getSeqCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSeqCount()\r
- {\r
- return _seqList.size();\r
- } //-- int getSeqCount() \r
+ public int getSeqCount(\r
+ ) {\r
+ return this._seqList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'start'.\r
* \r
- * @return int\r
- * @return the value of field 'start'.\r
+ * @return the value of field 'Start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart(\r
+ ) {\r
return this._start;\r
- } //-- int getStart() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol1'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol1'.\r
+ * @return the value of field 'TextCol1'.\r
*/\r
- public int getTextCol1()\r
- {\r
+ public int getTextCol1(\r
+ ) {\r
return this._textCol1;\r
- } //-- int getTextCol1() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol2'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol2'.\r
+ * @return the value of field 'TextCol2'.\r
*/\r
- public int getTextCol2()\r
- {\r
+ public int getTextCol2(\r
+ ) {\r
return this._textCol2;\r
- } //-- int getTextCol2() \r
+ }\r
\r
/**\r
* Returns the value of field 'textColThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'textColThreshold'.\r
+ * @return the value of field 'TextColThreshold'.\r
*/\r
- public int getTextColThreshold()\r
- {\r
+ public int getTextColThreshold(\r
+ ) {\r
return this._textColThreshold;\r
- } //-- int getTextColThreshold() \r
+ }\r
\r
/**\r
- * Method hasColourText\r
+ * Method hasColourText.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one ColourText has been added\r
*/\r
- public boolean hasColourText()\r
- {\r
+ public boolean hasColourText(\r
+ ) {\r
return this._has_colourText;\r
- } //-- boolean hasColourText() \r
+ }\r
\r
/**\r
- * Method hasConsThreshold\r
- * \r
+ * Method hasConsThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ConsThreshold has been added\r
*/\r
- public boolean hasConsThreshold()\r
- {\r
+ public boolean hasConsThreshold(\r
+ ) {\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ }\r
\r
/**\r
- * Method hasDisplayBoxes\r
- * \r
+ * Method hasDisplayBoxes.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one DisplayBoxes has been added\r
*/\r
- public boolean hasDisplayBoxes()\r
- {\r
+ public boolean hasDisplayBoxes(\r
+ ) {\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes() \r
+ }\r
\r
/**\r
- * Method hasDisplayText\r
- * \r
- * \r
+ * Method hasDisplayText.\r
* \r
- * @return boolean\r
+ * @return true if at least one DisplayText has been added\r
*/\r
- public boolean hasDisplayText()\r
- {\r
+ public boolean hasDisplayText(\r
+ ) {\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText() \r
+ }\r
\r
/**\r
- * Method hasEnd\r
- * \r
- * \r
+ * Method hasEnd.\r
* \r
- * @return boolean\r
+ * @return true if at least one End has been added\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd(\r
+ ) {\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ }\r
\r
/**\r
- * Method hasOutlineColour\r
+ * Method hasOutlineColour.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one OutlineColour has been added\r
*/\r
- public boolean hasOutlineColour()\r
- {\r
+ public boolean hasOutlineColour(\r
+ ) {\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour() \r
+ }\r
\r
/**\r
- * Method hasPidThreshold\r
- * \r
+ * Method hasPidThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one PidThreshold has been added\r
*/\r
- public boolean hasPidThreshold()\r
- {\r
+ public boolean hasPidThreshold(\r
+ ) {\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ }\r
\r
/**\r
- * Method hasStart\r
- * \r
+ * Method hasStart.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Start has been added\r
*/\r
- public boolean hasStart()\r
- {\r
+ public boolean hasStart(\r
+ ) {\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ }\r
\r
/**\r
- * Method hasTextCol1\r
- * \r
- * \r
+ * Method hasTextCol1.\r
* \r
- * @return boolean\r
+ * @return true if at least one TextCol1 has been added\r
*/\r
- public boolean hasTextCol1()\r
- {\r
+ public boolean hasTextCol1(\r
+ ) {\r
return this._has_textCol1;\r
- } //-- boolean hasTextCol1() \r
+ }\r
\r
/**\r
- * Method hasTextCol2\r
- * \r
- * \r
+ * Method hasTextCol2.\r
* \r
- * @return boolean\r
+ * @return true if at least one TextCol2 has been added\r
*/\r
- public boolean hasTextCol2()\r
- {\r
+ public boolean hasTextCol2(\r
+ ) {\r
return this._has_textCol2;\r
- } //-- boolean hasTextCol2() \r
+ }\r
\r
/**\r
- * Method hasTextColThreshold\r
+ * Method hasTextColThreshold.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one TextColThreshold has been added\r
*/\r
- public boolean hasTextColThreshold()\r
- {\r
+ public boolean hasTextColThreshold(\r
+ ) {\r
return this._has_textColThreshold;\r
- } //-- boolean hasTextColThreshold() \r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\r
+ * \r
+ * @return the value of field 'ColourText'.\r
+ */\r
+ public boolean isColourText(\r
+ ) {\r
+ return this._colourText;\r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Returns the value of field 'displayBoxes'.\r
* \r
+ * @return the value of field 'DisplayBoxes'.\r
+ */\r
+ public boolean isDisplayBoxes(\r
+ ) {\r
+ return this._displayBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayText'.\r
* \r
+ * @return the value of field 'DisplayText'.\r
+ */\r
+ public boolean isDisplayText(\r
+ ) {\r
+ return this._displayText;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllSeq\r
- * \r
*/\r
- public void removeAllSeq()\r
- {\r
- _seqList.removeAllElements();\r
- } //-- void removeAllSeq() \r
+ public void removeAllSeq(\r
+ ) {\r
+ this._seqList.clear();\r
+ }\r
\r
/**\r
- * Method removeSeq\r
- * \r
+ * Method removeSeq.\r
* \r
+ * @param vSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSeq(\r
+ final int vSeq) {\r
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSeqAt.\r
* \r
* @param index\r
- * @return int\r
+ * @return the element removed from the collection\r
*/\r
- public int removeSeq(int index)\r
- {\r
- java.lang.Object obj = _seqList.elementAt(index);\r
- _seqList.removeElementAt(index);\r
- return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeSeq(int) \r
+ public int removeSeqAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._seqList.remove(index);\r
+ return ((java.lang.Integer) obj).intValue();\r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(java.lang.String colour)\r
- {\r
+ public void setColour(\r
+ final java.lang.String colour) {\r
this._colour = colour;\r
- } //-- void setColour(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'colourText'.\r
* \r
* @param colourText the value of field 'colourText'.\r
*/\r
- public void setColourText(boolean colourText)\r
- {\r
+ public void setColourText(\r
+ final boolean colourText) {\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- } //-- void setColourText(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
* \r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
- {\r
+ public void setConsThreshold(\r
+ final int consThreshold) {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
* \r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
- public void setDisplayBoxes(boolean displayBoxes)\r
- {\r
+ public void setDisplayBoxes(\r
+ final boolean displayBoxes) {\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'displayText'.\r
* \r
* @param displayText the value of field 'displayText'.\r
*/\r
- public void setDisplayText(boolean displayText)\r
- {\r
+ public void setDisplayText(\r
+ final boolean displayText) {\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- } //-- void setDisplayText(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'end'.\r
* \r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(\r
+ final int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
* \r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
- public void setOutlineColour(int outlineColour)\r
- {\r
+ public void setOutlineColour(\r
+ final int outlineColour) {\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
* \r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
+ public void setPidThreshold(\r
+ final int pidThreshold) {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ }\r
\r
/**\r
- * Method setSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vSeq\r
- */\r
- public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSeq(\r
+ final int index,\r
+ final int vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size()) {\r
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
}\r
- _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int) \r
+ \r
+ this._seqList.set(index, new java.lang.Integer(vSeq));\r
+ }\r
\r
/**\r
- * Method setSeq\r
- * \r
* \r
* \r
- * @param seqArray\r
+ * @param vSeqArray\r
*/\r
- public void setSeq(int[] seqArray)\r
- {\r
+ public void setSeq(\r
+ final int[] vSeqArray) {\r
//-- copy array\r
- _seqList.removeAllElements();\r
- for (int i = 0; i < seqArray.length; i++) {\r
- _seqList.addElement(new java.lang.Integer(seqArray[i]));\r
+ _seqList.clear();\r
+ \r
+ for (int i = 0; i < vSeqArray.length; i++) {\r
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));\r
}\r
- } //-- void setSeq(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'start'.\r
* \r
* @param start the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(\r
+ final int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol1'.\r
* \r
* @param textCol1 the value of field 'textCol1'.\r
*/\r
- public void setTextCol1(int textCol1)\r
- {\r
+ public void setTextCol1(\r
+ final int textCol1) {\r
this._textCol1 = textCol1;\r
this._has_textCol1 = true;\r
- } //-- void setTextCol1(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol2'.\r
* \r
* @param textCol2 the value of field 'textCol2'.\r
*/\r
- public void setTextCol2(int textCol2)\r
- {\r
+ public void setTextCol2(\r
+ final int textCol2) {\r
this._textCol2 = textCol2;\r
this._has_textCol2 = true;\r
- } //-- void setTextCol2(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textColThreshold'.\r
* \r
* @param textColThreshold the value of field 'textColThreshold'\r
*/\r
- public void setTextColThreshold(int textColThreshold)\r
- {\r
+ public void setTextColThreshold(\r
+ final int textColThreshold) {\r
this._textColThreshold = textColThreshold;\r
this._has_textColThreshold = true;\r
- } //-- void setTextColThreshold(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.JGroup\r
+ */\r
+ public static jalview.schemabinding.version2.JGroup unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JSeq.\r
//--------------------------/\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private int _colour;\r
\r
private boolean _has_colour;\r
\r
/**\r
- * Field _start\r
+ * Field _start.\r
*/\r
private int _start;\r
\r
private boolean _has_start;\r
\r
/**\r
- * Field _end\r
+ * Field _end.\r
*/\r
private int _end;\r
\r
private boolean _has_end;\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private int _id;\r
\r
private boolean _has_id;\r
\r
/**\r
- * Field _hidden\r
+ * Field _hidden.\r
*/\r
private boolean _hidden;\r
\r
private boolean _has_hidden;\r
\r
/**\r
- * Field _featuresList\r
+ * Field _featuresList.\r
*/\r
private java.util.Vector _featuresList;\r
\r
/**\r
- * Field _pdbidsList\r
+ * Field _pdbidsList.\r
*/\r
private java.util.Vector _pdbidsList;\r
\r
/**\r
- * Field _hiddenSequencesList\r
+ * Field _hiddenSequencesList.\r
*/\r
private java.util.Vector _hiddenSequencesList;\r
\r
\r
public JSeq() {\r
super();\r
- _featuresList = new Vector();\r
- _pdbidsList = new Vector();\r
- _hiddenSequencesList = new Vector();\r
- } //-- jalview.schemabinding.version2.JSeq()\r
+ this._featuresList = new java.util.Vector();\r
+ this._pdbidsList = new java.util.Vector();\r
+ this._hiddenSequencesList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addFeatures\r
- * \r
* \r
* \r
* @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addFeatures(jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.addElement(vFeatures);\r
- } //-- void addFeatures(jalview.schemabinding.version2.Features) \r
+ public void addFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.addElement(vFeatures);\r
+ }\r
\r
/**\r
- * Method addFeatures\r
- * \r
* \r
* \r
* @param index\r
* @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.insertElementAt(vFeatures, index);\r
- } //-- void addFeatures(int, jalview.schemabinding.version2.Features) \r
+ public void addFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.add(index, vFeatures);\r
+ }\r
\r
/**\r
- * Method addHiddenSequences\r
- * \r
* \r
* \r
* @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addHiddenSequences(int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
- } //-- void addHiddenSequences(int) \r
+ public void addHiddenSequences(\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+ }\r
\r
/**\r
- * Method addHiddenSequences\r
- * \r
* \r
* \r
* @param index\r
* @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);\r
- } //-- void addHiddenSequences(int, int) \r
+ public void addHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
\r
/**\r
- * Method addPdbids\r
- * \r
* \r
* \r
* @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.addElement(vPdbids);\r
- } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) \r
+ public void addPdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.addElement(vPdbids);\r
+ }\r
\r
/**\r
- * Method addPdbids\r
- * \r
* \r
* \r
* @param index\r
* @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.insertElementAt(vPdbids, index);\r
- } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) \r
+ public void addPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.add(index, vPdbids);\r
+ }\r
\r
/**\r
- * Method deleteColour\r
- * \r
*/\r
- public void deleteColour()\r
- {\r
+ public void deleteColour(\r
+ ) {\r
this._has_colour= false;\r
- } //-- void deleteColour() \r
+ }\r
\r
/**\r
- * Method deleteEnd\r
- * \r
*/\r
- public void deleteEnd()\r
- {\r
+ public void deleteEnd(\r
+ ) {\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ }\r
\r
/**\r
- * Method deleteHidden\r
- * \r
*/\r
- public void deleteHidden()\r
- {\r
+ public void deleteHidden(\r
+ ) {\r
this._has_hidden= false;\r
- } //-- void deleteHidden() \r
+ }\r
\r
/**\r
- * Method deleteId\r
- * \r
*/\r
- public void deleteId()\r
- {\r
+ public void deleteId(\r
+ ) {\r
this._has_id= false;\r
- } //-- void deleteId() \r
+ }\r
\r
/**\r
- * Method deleteStart\r
- * \r
*/\r
- public void deleteStart()\r
- {\r
+ public void deleteStart(\r
+ ) {\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ }\r
\r
/**\r
- * Method enumerateFeatures\r
- * \r
- * \r
+ * Method enumerateFeatures.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Features elements\r
*/\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return _featuresList.elements();\r
- } //-- java.util.Enumeration enumerateFeatures() \r
+ public java.util.Enumeration enumerateFeatures(\r
+ ) {\r
+ return this._featuresList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateHiddenSequences\r
+ * Method enumerateHiddenSequences.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all int elements\r
*/\r
- public java.util.Enumeration enumerateHiddenSequences()\r
- {\r
- return _hiddenSequencesList.elements();\r
- } //-- java.util.Enumeration enumerateHiddenSequences() \r
+ public java.util.Enumeration enumerateHiddenSequences(\r
+ ) {\r
+ return this._hiddenSequencesList.elements();\r
+ }\r
\r
/**\r
- * Method enumeratePdbids\r
- * \r
+ * Method enumeratePdbids.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Pdbids elements\r
*/\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return _pdbidsList.elements();\r
- } //-- java.util.Enumeration enumeratePdbids() \r
+ public java.util.Enumeration enumeratePdbids(\r
+ ) {\r
+ return this._pdbidsList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return int\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public int getColour()\r
- {\r
+ public int getColour(\r
+ ) {\r
return this._colour;\r
- } //-- int getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'end'.\r
* \r
- * @return int\r
- * @return the value of field 'end'.\r
+ * @return the value of field 'End'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd(\r
+ ) {\r
return this._end;\r
- } //-- int getEnd() \r
+ }\r
\r
/**\r
- * Method getFeatures\r
- * \r
- * \r
+ * Method getFeatures.\r
* \r
* @param index\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features getFeatures(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _featuresList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Features at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Features getFeatures(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Features getFeatures(int) \r
+ return (jalview.schemabinding.version2.Features) _featuresList.get(index);\r
+ }\r
\r
/**\r
- * Method getFeatures\r
+ * Method getFeatures.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return Features\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Features[] getFeatures()\r
- {\r
- int size = _featuresList.size();\r
- jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Features[] getFeatures() \r
+ public jalview.schemabinding.version2.Features[] getFeatures(\r
+ ) {\r
+ jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];\r
+ return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getFeaturesCount\r
- * \r
- * \r
+ * Method getFeaturesCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getFeaturesCount()\r
- {\r
- return _featuresList.size();\r
- } //-- int getFeaturesCount() \r
+ public int getFeaturesCount(\r
+ ) {\r
+ return this._featuresList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'hidden'.\r
* \r
- * @return boolean\r
- * @return the value of field 'hidden'.\r
+ * @return the value of field 'Hidden'.\r
*/\r
- public boolean getHidden()\r
- {\r
+ public boolean getHidden(\r
+ ) {\r
return this._hidden;\r
- } //-- boolean getHidden() \r
+ }\r
\r
/**\r
- * Method getHiddenSequences\r
- * \r
- * \r
+ * Method getHiddenSequences.\r
* \r
* @param index\r
- * @return int\r
- */\r
- public int getHiddenSequences(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the int at the given index\r
+ */\r
+ public int getHiddenSequences(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
}\r
\r
- return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
- } //-- int getHiddenSequences(int) \r
+ return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();\r
+ }\r
\r
/**\r
- * Method getHiddenSequences\r
- * \r
- * \r
+ * Method getHiddenSequences.Returns the contents of the\r
+ * collection in an Array. \r
* \r
- * @return int\r
+ * @return this collection as an Array\r
*/\r
- public int[] getHiddenSequences()\r
- {\r
- int size = _hiddenSequencesList.size();\r
- int[] mArray = new int[size];\r
+ public int[] getHiddenSequences(\r
+ ) {\r
+ int size = this._hiddenSequencesList.size();\r
+ int[] array = new int[size];\r
+ java.util.Iterator iter = _hiddenSequencesList.iterator();\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+ array[index] = ((java.lang.Integer) iter.next()).intValue();\r
}\r
- return mArray;\r
- } //-- int[] getHiddenSequences() \r
+ return array;\r
+ }\r
\r
/**\r
- * Method getHiddenSequencesCount\r
+ * Method getHiddenSequencesCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getHiddenSequencesCount()\r
- {\r
- return _hiddenSequencesList.size();\r
- } //-- int getHiddenSequencesCount() \r
+ public int getHiddenSequencesCount(\r
+ ) {\r
+ return this._hiddenSequencesList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'id'.\r
* \r
- * @return int\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public int getId()\r
- {\r
+ public int getId(\r
+ ) {\r
return this._id;\r
- } //-- int getId() \r
+ }\r
\r
/**\r
- * Method getPdbids\r
- * \r
- * \r
+ * Method getPdbids.\r
* \r
* @param index\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids getPdbids(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _pdbidsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Pdbids at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids getPdbids(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) \r
+ return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);\r
+ }\r
\r
/**\r
- * Method getPdbids\r
- * \r
- * \r
+ * Method getPdbids.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return Pdbids\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
- {\r
- int size = _pdbidsList.size();\r
- jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() \r
+ public jalview.schemabinding.version2.Pdbids[] getPdbids(\r
+ ) {\r
+ jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];\r
+ return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getPdbidsCount\r
- * \r
+ * Method getPdbidsCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getPdbidsCount()\r
- {\r
- return _pdbidsList.size();\r
- } //-- int getPdbidsCount() \r
+ public int getPdbidsCount(\r
+ ) {\r
+ return this._pdbidsList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'start'.\r
* \r
- * @return int\r
- * @return the value of field 'start'.\r
+ * @return the value of field 'Start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart(\r
+ ) {\r
return this._start;\r
- } //-- int getStart() \r
+ }\r
\r
/**\r
- * Method hasColour\r
- * \r
- * \r
+ * Method hasColour.\r
* \r
- * @return boolean\r
+ * @return true if at least one Colour has been added\r
*/\r
- public boolean hasColour()\r
- {\r
+ public boolean hasColour(\r
+ ) {\r
return this._has_colour;\r
- } //-- boolean hasColour() \r
+ }\r
\r
/**\r
- * Method hasEnd\r
+ * Method hasEnd.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one End has been added\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd(\r
+ ) {\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ }\r
\r
/**\r
- * Method hasHidden\r
- * \r
+ * Method hasHidden.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Hidden has been added\r
*/\r
- public boolean hasHidden()\r
- {\r
+ public boolean hasHidden(\r
+ ) {\r
return this._has_hidden;\r
- } //-- boolean hasHidden() \r
+ }\r
\r
/**\r
- * Method hasId\r
- * \r
- * \r
+ * Method hasId.\r
* \r
- * @return boolean\r
+ * @return true if at least one Id has been added\r
*/\r
- public boolean hasId()\r
- {\r
+ public boolean hasId(\r
+ ) {\r
return this._has_id;\r
- } //-- boolean hasId() \r
+ }\r
\r
/**\r
- * Method hasStart\r
+ * Method hasStart.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Start has been added\r
*/\r
- public boolean hasStart()\r
- {\r
+ public boolean hasStart(\r
+ ) {\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Returns the value of field 'hidden'.\r
* \r
+ * @return the value of field 'Hidden'.\r
+ */\r
+ public boolean isHidden(\r
+ ) {\r
+ return this._hidden;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllFeatures\r
- * \r
*/\r
- public void removeAllFeatures()\r
- {\r
- _featuresList.removeAllElements();\r
- } //-- void removeAllFeatures() \r
+ public void removeAllFeatures(\r
+ ) {\r
+ this._featuresList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllHiddenSequences\r
- * \r
*/\r
- public void removeAllHiddenSequences()\r
- {\r
- _hiddenSequencesList.removeAllElements();\r
- } //-- void removeAllHiddenSequences() \r
+ public void removeAllHiddenSequences(\r
+ ) {\r
+ this._hiddenSequencesList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllPdbids\r
- * \r
*/\r
- public void removeAllPdbids()\r
- {\r
- _pdbidsList.removeAllElements();\r
- } //-- void removeAllPdbids() \r
+ public void removeAllPdbids(\r
+ ) {\r
+ this._pdbidsList.clear();\r
+ }\r
\r
/**\r
- * Method removeFeatures\r
- * \r
+ * Method removeFeatures.\r
* \r
+ * @param vFeatures\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures) {\r
+ boolean removed = _featuresList.remove(vFeatures);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeFeaturesAt.\r
* \r
* @param index\r
- * @return Features\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Features removeFeatures(int index)\r
- {\r
- java.lang.Object obj = _featuresList.elementAt(index);\r
- _featuresList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Features removeFeaturesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._featuresList.remove(index);\r
return (jalview.schemabinding.version2.Features) obj;\r
- } //-- jalview.schemabinding.version2.Features removeFeatures(int) \r
+ }\r
\r
/**\r
- * Method removeHiddenSequences\r
- * \r
+ * Method removeHiddenSequences.\r
* \r
+ * @param vHiddenSequences\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeHiddenSequences(\r
+ final int vHiddenSequences) {\r
+ boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenSequencesAt.\r
* \r
* @param index\r
- * @return int\r
+ * @return the element removed from the collection\r
*/\r
- public int removeHiddenSequences(int index)\r
- {\r
- java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
- _hiddenSequencesList.removeElementAt(index);\r
- return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeHiddenSequences(int) \r
+ public int removeHiddenSequencesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._hiddenSequencesList.remove(index);\r
+ return ((java.lang.Integer) obj).intValue();\r
+ }\r
\r
/**\r
- * Method removePdbids\r
- * \r
+ * Method removePdbids.\r
* \r
+ * @param vPdbids\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removePdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids) {\r
+ boolean removed = _pdbidsList.remove(vPdbids);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePdbidsAt.\r
* \r
* @param index\r
- * @return Pdbids\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Pdbids removePdbids(int index)\r
- {\r
- java.lang.Object obj = _pdbidsList.elementAt(index);\r
- _pdbidsList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Pdbids removePdbidsAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._pdbidsList.remove(index);\r
return (jalview.schemabinding.version2.Pdbids) obj;\r
- } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(int colour)\r
- {\r
+ public void setColour(\r
+ final int colour) {\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'end'.\r
* \r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(\r
+ final int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ }\r
\r
/**\r
- * Method setFeatures\r
- * \r
* \r
* \r
* @param index\r
* @param vFeatures\r
- */\r
- public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _featuresList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
}\r
- _featuresList.setElementAt(vFeatures, index);\r
- } //-- void setFeatures(int, jalview.schemabinding.version2.Features) \r
+ \r
+ this._featuresList.set(index, vFeatures);\r
+ }\r
\r
/**\r
- * Method setFeatures\r
- * \r
* \r
* \r
- * @param featuresArray\r
+ * @param vFeaturesArray\r
*/\r
- public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)\r
- {\r
+ public void setFeatures(\r
+ final jalview.schemabinding.version2.Features[] vFeaturesArray) {\r
//-- copy array\r
- _featuresList.removeAllElements();\r
- for (int i = 0; i < featuresArray.length; i++) {\r
- _featuresList.addElement(featuresArray[i]);\r
+ _featuresList.clear();\r
+ \r
+ for (int i = 0; i < vFeaturesArray.length; i++) {\r
+ this._featuresList.add(vFeaturesArray[i]);\r
}\r
- } //-- void setFeatures(jalview.schemabinding.version2.Features) \r
+ }\r
\r
/**\r
* Sets the value of field 'hidden'.\r
* \r
* @param hidden the value of field 'hidden'.\r
*/\r
- public void setHidden(boolean hidden)\r
- {\r
+ public void setHidden(\r
+ final boolean hidden) {\r
this._hidden = hidden;\r
this._has_hidden = true;\r
- } //-- void setHidden(boolean) \r
+ }\r
\r
/**\r
- * Method setHiddenSequences\r
- * \r
* \r
* \r
* @param index\r
* @param vHiddenSequences\r
- */\r
- public void setHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
}\r
- _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);\r
- } //-- void setHiddenSequences(int, int) \r
+ \r
+ this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
\r
/**\r
- * Method setHiddenSequences\r
- * \r
* \r
* \r
- * @param hiddenSequencesArray\r
+ * @param vHiddenSequencesArray\r
*/\r
- public void setHiddenSequences(int[] hiddenSequencesArray)\r
- {\r
+ public void setHiddenSequences(\r
+ final int[] vHiddenSequencesArray) {\r
//-- copy array\r
- _hiddenSequencesList.removeAllElements();\r
- for (int i = 0; i < hiddenSequencesArray.length; i++) {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));\r
+ _hiddenSequencesList.clear();\r
+ \r
+ for (int i = 0; i < vHiddenSequencesArray.length; i++) {\r
+ this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));\r
}\r
- } //-- void setHiddenSequences(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(int id)\r
- {\r
+ public void setId(\r
+ final int id) {\r
this._id = id;\r
this._has_id = true;\r
- } //-- void setId(int) \r
+ }\r
\r
/**\r
- * Method setPdbids\r
- * \r
* \r
* \r
* @param index\r
* @param vPdbids\r
- */\r
- public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _pdbidsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
}\r
- _pdbidsList.setElementAt(vPdbids, index);\r
- } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) \r
+ \r
+ this._pdbidsList.set(index, vPdbids);\r
+ }\r
\r
/**\r
- * Method setPdbids\r
* \r
* \r
- * \r
- * @param pdbidsArray\r
+ * @param vPdbidsArray\r
*/\r
- public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)\r
- {\r
+ public void setPdbids(\r
+ final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {\r
//-- copy array\r
- _pdbidsList.removeAllElements();\r
- for (int i = 0; i < pdbidsArray.length; i++) {\r
- _pdbidsList.addElement(pdbidsArray[i]);\r
+ _pdbidsList.clear();\r
+ \r
+ for (int i = 0; i < vPdbidsArray.length; i++) {\r
+ this._pdbidsList.add(vPdbidsArray[i]);\r
}\r
- } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) \r
+ }\r
\r
/**\r
* Sets the value of field 'start'.\r
* \r
* @param start the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(\r
+ final int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.JSeq\r
+ */\r
+ public static jalview.schemabinding.version2.JSeq unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Date;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JalviewModel.\r
//--------------------------/\r
\r
/**\r
- * Field _creationDate\r
+ * Field _creationDate.\r
*/\r
private java.util.Date _creationDate;\r
\r
/**\r
- * Field _version\r
+ * Field _version.\r
*/\r
private java.lang.String _version;\r
\r
/**\r
- * Field _vamsasModel\r
+ * Field _vamsasModel.\r
*/\r
private jalview.schemabinding.version2.VamsasModel _vamsasModel;\r
\r
/**\r
- * Field _jalviewModelSequence\r
+ * Field _jalviewModelSequence.\r
*/\r
private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;\r
\r
\r
public JalviewModel() {\r
super();\r
- } //-- jalview.schemabinding.version2.JalviewModel()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'creationDate'.\r
* \r
- * @return Date\r
- * @return the value of field 'creationDate'.\r
+ * @return the value of field 'CreationDate'.\r
*/\r
- public java.util.Date getCreationDate()\r
- {\r
+ public java.util.Date getCreationDate(\r
+ ) {\r
return this._creationDate;\r
- } //-- java.util.Date getCreationDate() \r
+ }\r
\r
/**\r
* Returns the value of field 'jalviewModelSequence'.\r
* \r
- * @return JalviewModelSequence\r
- * @return the value of field 'jalviewModelSequence'.\r
+ * @return the value of field 'JalviewModelSequence'.\r
*/\r
- public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()\r
- {\r
+ public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence(\r
+ ) {\r
return this._jalviewModelSequence;\r
- } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() \r
+ }\r
\r
/**\r
* Returns the value of field 'vamsasModel'.\r
* \r
- * @return VamsasModel\r
- * @return the value of field 'vamsasModel'.\r
+ * @return the value of field 'VamsasModel'.\r
*/\r
- public jalview.schemabinding.version2.VamsasModel getVamsasModel()\r
- {\r
+ public jalview.schemabinding.version2.VamsasModel getVamsasModel(\r
+ ) {\r
return this._vamsasModel;\r
- } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel() \r
+ }\r
\r
/**\r
* Returns the value of field 'version'.\r
* \r
- * @return String\r
- * @return the value of field 'version'.\r
+ * @return the value of field 'Version'.\r
*/\r
- public java.lang.String getVersion()\r
- {\r
+ public java.lang.String getVersion(\r
+ ) {\r
return this._version;\r
- } //-- java.lang.String getVersion() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'creationDate'.\r
* \r
* @param creationDate the value of field 'creationDate'.\r
*/\r
- public void setCreationDate(java.util.Date creationDate)\r
- {\r
+ public void setCreationDate(\r
+ final java.util.Date creationDate) {\r
this._creationDate = creationDate;\r
- } //-- void setCreationDate(java.util.Date) \r
+ }\r
\r
/**\r
* Sets the value of field 'jalviewModelSequence'.\r
* @param jalviewModelSequence the value of field\r
* 'jalviewModelSequence'.\r
*/\r
- public void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)\r
- {\r
+ public void setJalviewModelSequence(\r
+ final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) {\r
this._jalviewModelSequence = jalviewModelSequence;\r
- } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence) \r
+ }\r
\r
/**\r
* Sets the value of field 'vamsasModel'.\r
* \r
* @param vamsasModel the value of field 'vamsasModel'.\r
*/\r
- public void setVamsasModel(jalview.schemabinding.version2.VamsasModel vamsasModel)\r
- {\r
+ public void setVamsasModel(\r
+ final jalview.schemabinding.version2.VamsasModel vamsasModel) {\r
this._vamsasModel = vamsasModel;\r
- } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel) \r
+ }\r
\r
/**\r
* Sets the value of field 'version'.\r
* \r
* @param version the value of field 'version'.\r
*/\r
- public void setVersion(java.lang.String version)\r
- {\r
+ public void setVersion(\r
+ final java.lang.String version) {\r
this._version = version;\r
- } //-- void setVersion(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.JalviewModel\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewModel unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JalviewModelSequence.\r
//--------------------------/\r
\r
/**\r
- * Field _JSeqList\r
+ * Field _JSeqList.\r
*/\r
private java.util.Vector _JSeqList;\r
\r
/**\r
- * Field _JGroupList\r
+ * Field _JGroupList.\r
*/\r
private java.util.Vector _JGroupList;\r
\r
/**\r
- * Field _viewportList\r
+ * Field _viewportList.\r
*/\r
private java.util.Vector _viewportList;\r
\r
/**\r
- * Field _userColoursList\r
+ * Field _userColoursList.\r
*/\r
private java.util.Vector _userColoursList;\r
\r
/**\r
- * Field _treeList\r
+ * Field _treeList.\r
*/\r
private java.util.Vector _treeList;\r
\r
/**\r
- * Field _featureSettings\r
+ * Field _featureSettings.\r
*/\r
private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
\r
\r
public JalviewModelSequence() {\r
super();\r
- _JSeqList = new Vector();\r
- _JGroupList = new Vector();\r
- _viewportList = new Vector();\r
- _userColoursList = new Vector();\r
- _treeList = new Vector();\r
- } //-- jalview.schemabinding.version2.JalviewModelSequence()\r
+ this._JSeqList = new java.util.Vector();\r
+ this._JGroupList = new java.util.Vector();\r
+ this._viewportList = new java.util.Vector();\r
+ this._userColoursList = new java.util.Vector();\r
+ this._treeList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addJGroup\r
- * \r
* \r
* \r
* @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.schemabinding.version2.JGroup) \r
+ public void addJGroup(\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JGroupList.addElement(vJGroup);\r
+ }\r
\r
/**\r
- * Method addJGroup\r
- * \r
* \r
* \r
* @param index\r
* @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup) \r
+ public void addJGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JGroupList.add(index, vJGroup);\r
+ }\r
\r
/**\r
- * Method addJSeq\r
- * \r
* \r
* \r
* @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.schemabinding.version2.JSeq) \r
+ public void addJSeq(\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JSeqList.addElement(vJSeq);\r
+ }\r
\r
/**\r
- * Method addJSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq) \r
+ public void addJSeq(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JSeqList.add(index, vJSeq);\r
+ }\r
\r
/**\r
- * Method addTree\r
- * \r
* \r
* \r
* @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addTree(jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(jalview.schemabinding.version2.Tree) \r
+ public void addTree(\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.addElement(vTree);\r
+ }\r
\r
/**\r
- * Method addTree\r
- * \r
* \r
* \r
* @param index\r
* @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addTree(int index, jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, jalview.schemabinding.version2.Tree) \r
+ public void addTree(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.add(index, vTree);\r
+ }\r
\r
/**\r
- * Method addUserColours\r
- * \r
* \r
* \r
* @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addUserColours(jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.schemabinding.version2.UserColours) \r
+ public void addUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._userColoursList.addElement(vUserColours);\r
+ }\r
\r
/**\r
- * Method addUserColours\r
- * \r
* \r
* \r
* @param index\r
* @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours) \r
+ public void addUserColours(\r
+ final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._userColoursList.add(index, vUserColours);\r
+ }\r
\r
/**\r
- * Method addViewport\r
- * \r
* \r
* \r
* @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addViewport(jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.schemabinding.version2.Viewport) \r
+ public void addViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._viewportList.addElement(vViewport);\r
+ }\r
\r
/**\r
- * Method addViewport\r
- * \r
* \r
* \r
* @param index\r
* @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addViewport(int index, jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.schemabinding.version2.Viewport) \r
+ public void addViewport(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._viewportList.add(index, vViewport);\r
+ }\r
\r
/**\r
- * Method enumerateJGroup\r
- * \r
- * \r
+ * Method enumerateJGroup.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.JGroup elements\r
*/\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
- return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup() \r
+ public java.util.Enumeration enumerateJGroup(\r
+ ) {\r
+ return this._JGroupList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateJSeq\r
+ * Method enumerateJSeq.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.JSeq elements\r
*/\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
- return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq() \r
+ public java.util.Enumeration enumerateJSeq(\r
+ ) {\r
+ return this._JSeqList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateTree\r
- * \r
- * \r
+ * Method enumerateTree.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Tree elements\r
*/\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
+ public java.util.Enumeration enumerateTree(\r
+ ) {\r
+ return this._treeList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateUserColours\r
+ * Method enumerateUserColours.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.UserColours elements\r
*/\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
- return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours() \r
+ public java.util.Enumeration enumerateUserColours(\r
+ ) {\r
+ return this._userColoursList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateViewport\r
- * \r
- * \r
+ * Method enumerateViewport.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Viewport elements\r
*/\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
- return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport() \r
+ public java.util.Enumeration enumerateViewport(\r
+ ) {\r
+ return this._viewportList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'featureSettings'.\r
* \r
- * @return FeatureSettings\r
- * @return the value of field 'featureSettings'.\r
+ * @return the value of field 'FeatureSettings'.\r
*/\r
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
- {\r
+ public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(\r
+ ) {\r
return this._featureSettings;\r
- } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings() \r
+ }\r
\r
/**\r
- * Method getJGroup\r
- * \r
- * \r
+ * Method getJGroup.\r
* \r
* @param index\r
- * @return JGroup\r
- */\r
- public jalview.schemabinding.version2.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JGroupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.JGroup at the given index\r
+ */\r
+ public jalview.schemabinding.version2.JGroup getJGroup(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size()) {\r
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.JGroup getJGroup(int) \r
+ return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
+ }\r
\r
/**\r
- * Method getJGroup\r
- * \r
- * \r
+ * Method getJGroup.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return JGroup\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.JGroup[] getJGroup()\r
- {\r
- int size = _JGroupList.size();\r
- jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.version2.JGroup[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.JGroup[] getJGroup() \r
+ public jalview.schemabinding.version2.JGroup[] getJGroup(\r
+ ) {\r
+ jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
+ return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getJGroupCount\r
- * \r
+ * Method getJGroupCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getJGroupCount()\r
- {\r
- return _JGroupList.size();\r
- } //-- int getJGroupCount() \r
+ public int getJGroupCount(\r
+ ) {\r
+ return this._JGroupList.size();\r
+ }\r
\r
/**\r
- * Method getJSeq\r
- * \r
- * \r
+ * Method getJSeq.\r
* \r
* @param index\r
- * @return JSeq\r
- */\r
- public jalview.schemabinding.version2.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JSeqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.JSeq\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.JSeq getJSeq(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size()) {\r
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.JSeq getJSeq(int) \r
+ return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
+ }\r
\r
/**\r
- * Method getJSeq\r
- * \r
- * \r
+ * Method getJSeq.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return JSeq\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.JSeq[] getJSeq()\r
- {\r
- int size = _JSeqList.size();\r
- jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.version2.JSeq[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.JSeq[] getJSeq() \r
+ public jalview.schemabinding.version2.JSeq[] getJSeq(\r
+ ) {\r
+ jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
+ return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getJSeqCount\r
- * \r
+ * Method getJSeqCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getJSeqCount()\r
- {\r
- return _JSeqList.size();\r
- } //-- int getJSeqCount() \r
+ public int getJSeqCount(\r
+ ) {\r
+ return this._JSeqList.size();\r
+ }\r
\r
/**\r
- * Method getTree\r
- * \r
- * \r
+ * Method getTree.\r
* \r
* @param index\r
- * @return Tree\r
- */\r
- public jalview.schemabinding.version2.Tree getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.Tree\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Tree getTree(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Tree getTree(int) \r
+ return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
+ }\r
\r
/**\r
- * Method getTree\r
- * \r
+ * Method getTree.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * @return Tree\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Tree[] getTree()\r
- {\r
- int size = _treeList.size();\r
- jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.version2.Tree[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Tree[] getTree() \r
+ public jalview.schemabinding.version2.Tree[] getTree(\r
+ ) {\r
+ jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
+ return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getTreeCount\r
+ * Method getTreeCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount() \r
+ public int getTreeCount(\r
+ ) {\r
+ return this._treeList.size();\r
+ }\r
\r
/**\r
- * Method getUserColours\r
- * \r
- * \r
+ * Method getUserColours.\r
* \r
* @param index\r
- * @return UserColours\r
- */\r
- public jalview.schemabinding.version2.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _userColoursList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.UserColours at the given index\r
+ */\r
+ public jalview.schemabinding.version2.UserColours getUserColours(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size()) {\r
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.UserColours getUserColours(int) \r
+ return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);\r
+ }\r
\r
/**\r
- * Method getUserColours\r
+ * Method getUserColours.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return UserColours\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.UserColours[] getUserColours()\r
- {\r
- int size = _userColoursList.size();\r
- jalview.schemabinding.version2.UserColours[] mArray = new jalview.schemabinding.version2.UserColours[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.UserColours[] getUserColours() \r
+ public jalview.schemabinding.version2.UserColours[] getUserColours(\r
+ ) {\r
+ jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
+ return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getUserColoursCount\r
- * \r
+ * Method getUserColoursCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getUserColoursCount()\r
- {\r
- return _userColoursList.size();\r
- } //-- int getUserColoursCount() \r
+ public int getUserColoursCount(\r
+ ) {\r
+ return this._userColoursList.size();\r
+ }\r
\r
/**\r
- * Method getViewport\r
- * \r
- * \r
+ * Method getViewport.\r
* \r
* @param index\r
- * @return Viewport\r
- */\r
- public jalview.schemabinding.version2.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _viewportList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Viewport at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Viewport getViewport(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size()) {\r
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Viewport getViewport(int) \r
+ return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);\r
+ }\r
\r
/**\r
- * Method getViewport\r
- * \r
+ * Method getViewport.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * @return Viewport\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Viewport[] getViewport()\r
- {\r
- int size = _viewportList.size();\r
- jalview.schemabinding.version2.Viewport[] mArray = new jalview.schemabinding.version2.Viewport[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Viewport[] getViewport() \r
+ public jalview.schemabinding.version2.Viewport[] getViewport(\r
+ ) {\r
+ jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
+ return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getViewportCount\r
- * \r
- * \r
+ * Method getViewportCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getViewportCount()\r
- {\r
- return _viewportList.size();\r
- } //-- int getViewportCount() \r
+ public int getViewportCount(\r
+ ) {\r
+ return this._viewportList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllJGroup\r
- * \r
*/\r
- public void removeAllJGroup()\r
- {\r
- _JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup() \r
+ public void removeAllJGroup(\r
+ ) {\r
+ this._JGroupList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllJSeq\r
- * \r
*/\r
- public void removeAllJSeq()\r
- {\r
- _JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq() \r
+ public void removeAllJSeq(\r
+ ) {\r
+ this._JSeqList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllTree\r
- * \r
*/\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
+ public void removeAllTree(\r
+ ) {\r
+ this._treeList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllUserColours\r
- * \r
*/\r
- public void removeAllUserColours()\r
- {\r
- _userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours() \r
+ public void removeAllUserColours(\r
+ ) {\r
+ this._userColoursList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllViewport\r
- * \r
*/\r
- public void removeAllViewport()\r
- {\r
- _viewportList.removeAllElements();\r
- } //-- void removeAllViewport() \r
+ public void removeAllViewport(\r
+ ) {\r
+ this._viewportList.clear();\r
+ }\r
\r
/**\r
- * Method removeJGroup\r
- * \r
+ * Method removeJGroup.\r
* \r
+ * @param vJGroup\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJGroup(\r
+ final jalview.schemabinding.version2.JGroup vJGroup) {\r
+ boolean removed = _JGroupList.remove(vJGroup);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJGroupAt.\r
* \r
* @param index\r
- * @return JGroup\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.JGroup removeJGroup(int index)\r
- {\r
- java.lang.Object obj = _JGroupList.elementAt(index);\r
- _JGroupList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._JGroupList.remove(index);\r
return (jalview.schemabinding.version2.JGroup) obj;\r
- } //-- jalview.schemabinding.version2.JGroup removeJGroup(int) \r
+ }\r
\r
/**\r
- * Method removeJSeq\r
- * \r
+ * Method removeJSeq.\r
* \r
+ * @param vJSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJSeq(\r
+ final jalview.schemabinding.version2.JSeq vJSeq) {\r
+ boolean removed = _JSeqList.remove(vJSeq);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJSeqAt.\r
* \r
* @param index\r
- * @return JSeq\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.JSeq removeJSeq(int index)\r
- {\r
- java.lang.Object obj = _JSeqList.elementAt(index);\r
- _JSeqList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.JSeq removeJSeqAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._JSeqList.remove(index);\r
return (jalview.schemabinding.version2.JSeq) obj;\r
- } //-- jalview.schemabinding.version2.JSeq removeJSeq(int) \r
+ }\r
\r
/**\r
- * Method removeTree\r
- * \r
+ * Method removeTree.\r
* \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(\r
+ final jalview.schemabinding.version2.Tree vTree) {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
* \r
* @param index\r
- * @return Tree\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Tree removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Tree removeTreeAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
return (jalview.schemabinding.version2.Tree) obj;\r
- } //-- jalview.schemabinding.version2.Tree removeTree(int) \r
+ }\r
\r
/**\r
- * Method removeUserColours\r
- * \r
+ * Method removeUserColours.\r
* \r
+ * @param vUserColours\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours) {\r
+ boolean removed = _userColoursList.remove(vUserColours);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeUserColoursAt.\r
* \r
* @param index\r
- * @return UserColours\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.UserColours removeUserColours(int index)\r
- {\r
- java.lang.Object obj = _userColoursList.elementAt(index);\r
- _userColoursList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._userColoursList.remove(index);\r
return (jalview.schemabinding.version2.UserColours) obj;\r
- } //-- jalview.schemabinding.version2.UserColours removeUserColours(int) \r
+ }\r
\r
/**\r
- * Method removeViewport\r
- * \r
+ * Method removeViewport.\r
* \r
+ * @param vViewport\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport) {\r
+ boolean removed = _viewportList.remove(vViewport);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeViewportAt.\r
* \r
* @param index\r
- * @return Viewport\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Viewport removeViewport(int index)\r
- {\r
- java.lang.Object obj = _viewportList.elementAt(index);\r
- _viewportList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Viewport removeViewportAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._viewportList.remove(index);\r
return (jalview.schemabinding.version2.Viewport) obj;\r
- } //-- jalview.schemabinding.version2.Viewport removeViewport(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'featureSettings'.\r
* \r
* @param featureSettings the value of field 'featureSettings'.\r
*/\r
- public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings featureSettings)\r
- {\r
+ public void setFeatureSettings(\r
+ final jalview.schemabinding.version2.FeatureSettings featureSettings) {\r
this._featureSettings = featureSettings;\r
- } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings) \r
+ }\r
\r
/**\r
- * Method setJGroup\r
- * \r
* \r
* \r
* @param index\r
* @param vJGroup\r
- */\r
- public void setJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JGroupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setJGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size()) {\r
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
}\r
- _JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup) \r
+ \r
+ this._JGroupList.set(index, vJGroup);\r
+ }\r
\r
/**\r
- * Method setJGroup\r
* \r
* \r
- * \r
- * @param JGroupArray\r
+ * @param vJGroupArray\r
*/\r
- public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)\r
- {\r
+ public void setJGroup(\r
+ final jalview.schemabinding.version2.JGroup[] vJGroupArray) {\r
//-- copy array\r
- _JGroupList.removeAllElements();\r
- for (int i = 0; i < JGroupArray.length; i++) {\r
- _JGroupList.addElement(JGroupArray[i]);\r
+ _JGroupList.clear();\r
+ \r
+ for (int i = 0; i < vJGroupArray.length; i++) {\r
+ this._JGroupList.add(vJGroupArray[i]);\r
}\r
- } //-- void setJGroup(jalview.schemabinding.version2.JGroup) \r
+ }\r
\r
/**\r
- * Method setJSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vJSeq\r
- */\r
- public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JSeqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setJSeq(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size()) {\r
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
}\r
- _JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq) \r
+ \r
+ this._JSeqList.set(index, vJSeq);\r
+ }\r
\r
/**\r
- * Method setJSeq\r
- * \r
* \r
* \r
- * @param JSeqArray\r
+ * @param vJSeqArray\r
*/\r
- public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)\r
- {\r
+ public void setJSeq(\r
+ final jalview.schemabinding.version2.JSeq[] vJSeqArray) {\r
//-- copy array\r
- _JSeqList.removeAllElements();\r
- for (int i = 0; i < JSeqArray.length; i++) {\r
- _JSeqList.addElement(JSeqArray[i]);\r
+ _JSeqList.clear();\r
+ \r
+ for (int i = 0; i < vJSeqArray.length; i++) {\r
+ this._JSeqList.add(vJSeqArray[i]);\r
}\r
- } //-- void setJSeq(jalview.schemabinding.version2.JSeq) \r
+ }\r
\r
/**\r
- * Method setTree\r
- * \r
* \r
* \r
* @param index\r
* @param vTree\r
- */\r
- public void setTree(int index, jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setTree(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, jalview.schemabinding.version2.Tree) \r
+ \r
+ this._treeList.set(index, vTree);\r
+ }\r
\r
/**\r
- * Method setTree\r
- * \r
* \r
* \r
- * @param treeArray\r
+ * @param vTreeArray\r
*/\r
- public void setTree(jalview.schemabinding.version2.Tree[] treeArray)\r
- {\r
+ public void setTree(\r
+ final jalview.schemabinding.version2.Tree[] vTreeArray) {\r
//-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++) {\r
- _treeList.addElement(treeArray[i]);\r
+ _treeList.clear();\r
+ \r
+ for (int i = 0; i < vTreeArray.length; i++) {\r
+ this._treeList.add(vTreeArray[i]);\r
}\r
- } //-- void setTree(jalview.schemabinding.version2.Tree) \r
+ }\r
\r
/**\r
- * Method setUserColours\r
- * \r
* \r
* \r
* @param index\r
* @param vUserColours\r
- */\r
- public void setUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _userColoursList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setUserColours(\r
+ final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size()) {\r
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
}\r
- _userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours) \r
+ \r
+ this._userColoursList.set(index, vUserColours);\r
+ }\r
\r
/**\r
- * Method setUserColours\r
* \r
* \r
- * \r
- * @param userColoursArray\r
+ * @param vUserColoursArray\r
*/\r
- public void setUserColours(jalview.schemabinding.version2.UserColours[] userColoursArray)\r
- {\r
+ public void setUserColours(\r
+ final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {\r
//-- copy array\r
- _userColoursList.removeAllElements();\r
- for (int i = 0; i < userColoursArray.length; i++) {\r
- _userColoursList.addElement(userColoursArray[i]);\r
+ _userColoursList.clear();\r
+ \r
+ for (int i = 0; i < vUserColoursArray.length; i++) {\r
+ this._userColoursList.add(vUserColoursArray[i]);\r
}\r
- } //-- void setUserColours(jalview.schemabinding.version2.UserColours) \r
+ }\r
\r
/**\r
- * Method setViewport\r
- * \r
* \r
* \r
* @param index\r
* @param vViewport\r
- */\r
- public void setViewport(int index, jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _viewportList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setViewport(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size()) {\r
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
}\r
- _viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.schemabinding.version2.Viewport) \r
+ \r
+ this._viewportList.set(index, vViewport);\r
+ }\r
\r
/**\r
- * Method setViewport\r
- * \r
* \r
* \r
- * @param viewportArray\r
+ * @param vViewportArray\r
*/\r
- public void setViewport(jalview.schemabinding.version2.Viewport[] viewportArray)\r
- {\r
+ public void setViewport(\r
+ final jalview.schemabinding.version2.Viewport[] vViewportArray) {\r
//-- copy array\r
- _viewportList.removeAllElements();\r
- for (int i = 0; i < viewportArray.length; i++) {\r
- _viewportList.addElement(viewportArray[i]);\r
+ _viewportList.clear();\r
+ \r
+ for (int i = 0; i < vViewportArray.length; i++) {\r
+ this._viewportList.add(vViewportArray[i]);\r
}\r
- } //-- void setViewport(jalview.schemabinding.version2.Viewport) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.JalviewModelSequence\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JalviewUserColours.\r
//--------------------------/\r
\r
/**\r
- * Field _schemeName\r
+ * Field _schemeName.\r
*/\r
private java.lang.String _schemeName;\r
\r
/**\r
- * Field _colourList\r
+ * Field _colourList.\r
*/\r
private java.util.Vector _colourList;\r
\r
\r
public JalviewUserColours() {\r
super();\r
- _colourList = new Vector();\r
- } //-- jalview.schemabinding.version2.JalviewUserColours()\r
+ this._colourList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addColour\r
- * \r
* \r
* \r
* @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addColour(jalview.schemabinding.version2.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _colourList.addElement(vColour);\r
- } //-- void addColour(jalview.schemabinding.version2.Colour) \r
+ public void addColour(\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._colourList.addElement(vColour);\r
+ }\r
\r
/**\r
- * Method addColour\r
- * \r
* \r
* \r
* @param index\r
* @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addColour(int index, jalview.schemabinding.version2.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _colourList.insertElementAt(vColour, index);\r
- } //-- void addColour(int, jalview.schemabinding.version2.Colour) \r
+ public void addColour(\r
+ final int index,\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._colourList.add(index, vColour);\r
+ }\r
\r
/**\r
- * Method enumerateColour\r
- * \r
- * \r
+ * Method enumerateColour.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all Colour elements\r
*/\r
- public java.util.Enumeration enumerateColour()\r
- {\r
- return _colourList.elements();\r
- } //-- java.util.Enumeration enumerateColour() \r
+ public java.util.Enumeration enumerateColour(\r
+ ) {\r
+ return this._colourList.elements();\r
+ }\r
\r
/**\r
- * Method getColour\r
- * \r
- * \r
+ * Method getColour.\r
* \r
* @param index\r
- * @return Colour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the Colour at the given index\r
*/\r
- public jalview.schemabinding.version2.Colour getColour(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public Colour getColour(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._colourList.size()) {\r
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Colour getColour(int) \r
+ return (Colour) _colourList.get(index);\r
+ }\r
\r
/**\r
- * Method getColour\r
- * \r
- * \r
+ * Method getColour.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return Colour\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Colour[] getColour()\r
- {\r
- int size = _colourList.size();\r
- jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.version2.Colour[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Colour[] getColour() \r
+ public Colour[] getColour(\r
+ ) {\r
+ Colour[] array = new Colour[0];\r
+ return (Colour[]) this._colourList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getColourCount\r
- * \r
+ * Method getColourCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getColourCount()\r
- {\r
- return _colourList.size();\r
- } //-- int getColourCount() \r
+ public int getColourCount(\r
+ ) {\r
+ return this._colourList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'schemeName'.\r
* \r
- * @return String\r
- * @return the value of field 'schemeName'.\r
+ * @return the value of field 'SchemeName'.\r
*/\r
- public java.lang.String getSchemeName()\r
- {\r
+ public java.lang.String getSchemeName(\r
+ ) {\r
return this._schemeName;\r
- } //-- java.lang.String getSchemeName() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllColour\r
- * \r
*/\r
- public void removeAllColour()\r
- {\r
- _colourList.removeAllElements();\r
- } //-- void removeAllColour() \r
+ public void removeAllColour(\r
+ ) {\r
+ this._colourList.clear();\r
+ }\r
\r
/**\r
- * Method removeColour\r
- * \r
+ * Method removeColour.\r
* \r
+ * @param vColour\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeColour(\r
+ final Colour vColour) {\r
+ boolean removed = _colourList.remove(vColour);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeColourAt.\r
* \r
* @param index\r
- * @return Colour\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Colour removeColour(int index)\r
- {\r
- java.lang.Object obj = _colourList.elementAt(index);\r
- _colourList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Colour) obj;\r
- } //-- jalview.schemabinding.version2.Colour removeColour(int) \r
+ public Colour removeColourAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._colourList.remove(index);\r
+ return (Colour) obj;\r
+ }\r
\r
/**\r
- * Method setColour\r
- * \r
* \r
* \r
* @param index\r
* @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setColour(int index, jalview.schemabinding.version2.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setColour(\r
+ final int index,\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._colourList.size()) {\r
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");\r
}\r
- _colourList.setElementAt(vColour, index);\r
- } //-- void setColour(int, jalview.schemabinding.version2.Colour) \r
+ \r
+ this._colourList.set(index, vColour);\r
+ }\r
\r
/**\r
- * Method setColour\r
* \r
* \r
- * \r
- * @param colourArray\r
+ * @param vColourArray\r
*/\r
- public void setColour(jalview.schemabinding.version2.Colour[] colourArray)\r
- {\r
+ public void setColour(\r
+ final Colour[] vColourArray) {\r
//-- copy array\r
- _colourList.removeAllElements();\r
- for (int i = 0; i < colourArray.length; i++) {\r
- _colourList.addElement(colourArray[i]);\r
+ _colourList.clear();\r
+ \r
+ for (int i = 0; i < vColourArray.length; i++) {\r
+ this._colourList.add(vColourArray[i]);\r
}\r
- } //-- void setColour(jalview.schemabinding.version2.Colour) \r
+ }\r
\r
/**\r
* Sets the value of field 'schemeName'.\r
* \r
* @param schemeName the value of field 'schemeName'.\r
*/\r
- public void setSchemeName(java.lang.String schemeName)\r
- {\r
+ public void setSchemeName(\r
+ final java.lang.String schemeName) {\r
this._schemeName = schemeName;\r
- } //-- void setSchemeName(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.JalviewUserColours\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class OtherData.\r
//--------------------------/\r
\r
/**\r
- * Field _key\r
+ * Field _key.\r
*/\r
private java.lang.String _key;\r
\r
/**\r
- * Field _value\r
+ * Field _value.\r
*/\r
private java.lang.String _value;\r
\r
\r
public OtherData() {\r
super();\r
- } //-- jalview.schemabinding.version2.OtherData()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'key'.\r
* \r
- * @return String\r
- * @return the value of field 'key'.\r
+ * @return the value of field 'Key'.\r
*/\r
- public java.lang.String getKey()\r
- {\r
+ public java.lang.String getKey(\r
+ ) {\r
return this._key;\r
- } //-- java.lang.String getKey() \r
+ }\r
\r
/**\r
* Returns the value of field 'value'.\r
* \r
- * @return String\r
- * @return the value of field 'value'.\r
+ * @return the value of field 'Value'.\r
*/\r
- public java.lang.String getValue()\r
- {\r
+ public java.lang.String getValue(\r
+ ) {\r
return this._value;\r
- } //-- java.lang.String getValue() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'key'.\r
* \r
* @param key the value of field 'key'.\r
*/\r
- public void setKey(java.lang.String key)\r
- {\r
+ public void setKey(\r
+ final java.lang.String key) {\r
this._key = key;\r
- } //-- void setKey(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'value'.\r
* \r
* @param value the value of field 'value'.\r
*/\r
- public void setValue(java.lang.String value)\r
- {\r
+ public void setValue(\r
+ final java.lang.String value) {\r
this._value = value;\r
- } //-- void setValue(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.OtherData\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.OtherData unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Pdbentry.\r
//--------------------------/\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private java.lang.String _id;\r
\r
/**\r
- * Field _type\r
+ * Field _type.\r
*/\r
private java.lang.String _type;\r
\r
/**\r
- * Field _file\r
+ * Field _file.\r
*/\r
private java.lang.String _file;\r
\r
/**\r
- * Field _items\r
+ * Field _items.\r
*/\r
private java.util.Vector _items;\r
\r
\r
public Pdbentry() {\r
super();\r
- _items = new Vector();\r
- } //-- jalview.schemabinding.version2.Pdbentry()\r
+ this._items = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addPdbentryItem\r
- * \r
* \r
* \r
* @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.addElement(vPdbentryItem);\r
- } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem) \r
+ public void addPdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._items.addElement(vPdbentryItem);\r
+ }\r
\r
/**\r
- * Method addPdbentryItem\r
- * \r
* \r
* \r
* @param index\r
* @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.insertElementAt(vPdbentryItem, index);\r
- } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) \r
+ public void addPdbentryItem(\r
+ final int index,\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._items.add(index, vPdbentryItem);\r
+ }\r
\r
/**\r
- * Method enumeratePdbentryItem\r
- * \r
- * \r
+ * Method enumeratePdbentryItem.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.PdbentryItem elements\r
*/\r
- public java.util.Enumeration enumeratePdbentryItem()\r
- {\r
- return _items.elements();\r
- } //-- java.util.Enumeration enumeratePdbentryItem() \r
+ public java.util.Enumeration enumeratePdbentryItem(\r
+ ) {\r
+ return this._items.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'file'.\r
* \r
- * @return String\r
- * @return the value of field 'file'.\r
+ * @return the value of field 'File'.\r
*/\r
- public java.lang.String getFile()\r
- {\r
+ public java.lang.String getFile(\r
+ ) {\r
return this._file;\r
- } //-- java.lang.String getFile() \r
+ }\r
\r
/**\r
* Returns the value of field 'id'.\r
* \r
- * @return String\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId(\r
+ ) {\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ }\r
\r
/**\r
- * Method getPdbentryItem\r
- * \r
- * \r
+ * Method getPdbentryItem.\r
* \r
* @param index\r
- * @return PdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.PdbentryItem at the given inde\r
*/\r
- public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._items.size()) {\r
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);\r
- } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int) \r
+ return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);\r
+ }\r
\r
/**\r
- * Method getPdbentryItem\r
- * \r
- * \r
- * \r
- * @return PdbentryItem\r
+ * Method getPdbentryItem.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()\r
- {\r
- int size = _items.size();\r
- jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.schemabinding.version2.PdbentryItem[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() \r
+ public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem(\r
+ ) {\r
+ jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];\r
+ return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array);\r
+ }\r
\r
/**\r
- * Method getPdbentryItemCount\r
- * \r
- * \r
+ * Method getPdbentryItemCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getPdbentryItemCount()\r
- {\r
- return _items.size();\r
- } //-- int getPdbentryItemCount() \r
+ public int getPdbentryItemCount(\r
+ ) {\r
+ return this._items.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'type'.\r
* \r
- * @return String\r
- * @return the value of field 'type'.\r
+ * @return the value of field 'Type'.\r
*/\r
- public java.lang.String getType()\r
- {\r
+ public java.lang.String getType(\r
+ ) {\r
return this._type;\r
- } //-- java.lang.String getType() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllPdbentryItem\r
- * \r
*/\r
- public void removeAllPdbentryItem()\r
- {\r
- _items.removeAllElements();\r
- } //-- void removeAllPdbentryItem() \r
+ public void removeAllPdbentryItem(\r
+ ) {\r
+ this._items.clear();\r
+ }\r
\r
/**\r
- * Method removePdbentryItem\r
- * \r
+ * Method removePdbentryItem.\r
* \r
+ * @param vPdbentryItem\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removePdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) {\r
+ boolean removed = _items.remove(vPdbentryItem);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePdbentryItemAt.\r
* \r
* @param index\r
- * @return PdbentryItem\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int index)\r
- {\r
- java.lang.Object obj = _items.elementAt(index);\r
- _items.removeElementAt(index);\r
+ public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._items.remove(index);\r
return (jalview.schemabinding.version2.PdbentryItem) obj;\r
- } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'file'.\r
* \r
* @param file the value of field 'file'.\r
*/\r
- public void setFile(java.lang.String file)\r
- {\r
+ public void setFile(\r
+ final java.lang.String file) {\r
this._file = file;\r
- } //-- void setFile(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(\r
+ final java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ }\r
\r
/**\r
- * Method setPdbentryItem\r
- * \r
* \r
* \r
* @param index\r
* @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setPdbentryItem(\r
+ final int index,\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._items.size()) {\r
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");\r
}\r
- _items.setElementAt(vPdbentryItem, index);\r
- } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) \r
+ \r
+ this._items.set(index, vPdbentryItem);\r
+ }\r
\r
/**\r
- * Method setPdbentryItem\r
- * \r
* \r
* \r
- * @param pdbentryItemArray\r
+ * @param vPdbentryItemArray\r
*/\r
- public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray)\r
- {\r
+ public void setPdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) {\r
//-- copy array\r
- _items.removeAllElements();\r
- for (int i = 0; i < pdbentryItemArray.length; i++) {\r
- _items.addElement(pdbentryItemArray[i]);\r
+ _items.clear();\r
+ \r
+ for (int i = 0; i < vPdbentryItemArray.length; i++) {\r
+ this._items.add(vPdbentryItemArray[i]);\r
}\r
- } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem) \r
+ }\r
\r
/**\r
* Sets the value of field 'type'.\r
* \r
* @param type the value of field 'type'.\r
*/\r
- public void setType(java.lang.String type)\r
- {\r
+ public void setType(\r
+ final java.lang.String type) {\r
this._type = type;\r
- } //-- void setType(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Pdbentry\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Serializable;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
/**\r
* Class PdbentryItem.\r
* \r
//--------------------------/\r
\r
/**\r
- * Field _propertyList\r
+ * Field _propertyList.\r
*/\r
private java.util.Vector _propertyList;\r
\r
\r
public PdbentryItem() {\r
super();\r
- _propertyList = new Vector();\r
- } //-- jalview.schemabinding.version2.PdbentryItem()\r
+ this._propertyList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addProperty\r
- * \r
* \r
* \r
* @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addProperty(jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.addElement(vProperty);\r
- } //-- void addProperty(jalview.schemabinding.version2.Property) \r
+ public void addProperty(\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.addElement(vProperty);\r
+ }\r
\r
/**\r
- * Method addProperty\r
- * \r
* \r
* \r
* @param index\r
* @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addProperty(int index, jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.insertElementAt(vProperty, index);\r
- } //-- void addProperty(int, jalview.schemabinding.version2.Property) \r
+ public void addProperty(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.add(index, vProperty);\r
+ }\r
\r
/**\r
- * Method enumerateProperty\r
- * \r
- * \r
+ * Method enumerateProperty.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Property elements\r
*/\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return _propertyList.elements();\r
- } //-- java.util.Enumeration enumerateProperty() \r
+ public java.util.Enumeration enumerateProperty(\r
+ ) {\r
+ return this._propertyList.elements();\r
+ }\r
\r
/**\r
- * Method getProperty\r
- * \r
- * \r
+ * Method getProperty.\r
* \r
* @param index\r
- * @return Property\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Property at the given index\r
*/\r
- public jalview.schemabinding.version2.Property getProperty(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.Property getProperty(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Property getProperty(int) \r
+ return (jalview.schemabinding.version2.Property) _propertyList.get(index);\r
+ }\r
\r
/**\r
- * Method getProperty\r
- * \r
+ * Method getProperty.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * @return Property\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Property[] getProperty()\r
- {\r
- int size = _propertyList.size();\r
- jalview.schemabinding.version2.Property[] mArray = new jalview.schemabinding.version2.Property[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Property[] getProperty() \r
+ public jalview.schemabinding.version2.Property[] getProperty(\r
+ ) {\r
+ jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];\r
+ return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getPropertyCount\r
- * \r
+ * Method getPropertyCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getPropertyCount()\r
- {\r
- return _propertyList.size();\r
- } //-- int getPropertyCount() \r
+ public int getPropertyCount(\r
+ ) {\r
+ return this._propertyList.size();\r
+ }\r
\r
/**\r
- * Method removeAllProperty\r
- * \r
*/\r
- public void removeAllProperty()\r
- {\r
- _propertyList.removeAllElements();\r
- } //-- void removeAllProperty() \r
+ public void removeAllProperty(\r
+ ) {\r
+ this._propertyList.clear();\r
+ }\r
\r
/**\r
- * Method removeProperty\r
- * \r
+ * Method removeProperty.\r
* \r
+ * @param vProperty\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeProperty(\r
+ final jalview.schemabinding.version2.Property vProperty) {\r
+ boolean removed = _propertyList.remove(vProperty);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePropertyAt.\r
* \r
* @param index\r
- * @return Property\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Property removeProperty(int index)\r
- {\r
- java.lang.Object obj = _propertyList.elementAt(index);\r
- _propertyList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Property removePropertyAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._propertyList.remove(index);\r
return (jalview.schemabinding.version2.Property) obj;\r
- } //-- jalview.schemabinding.version2.Property removeProperty(int) \r
+ }\r
\r
/**\r
- * Method setProperty\r
- * \r
* \r
* \r
* @param index\r
* @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setProperty(int index, jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setProperty(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
}\r
- _propertyList.setElementAt(vProperty, index);\r
- } //-- void setProperty(int, jalview.schemabinding.version2.Property) \r
+ \r
+ this._propertyList.set(index, vProperty);\r
+ }\r
\r
/**\r
- * Method setProperty\r
* \r
* \r
- * \r
- * @param propertyArray\r
+ * @param vPropertyArray\r
*/\r
- public void setProperty(jalview.schemabinding.version2.Property[] propertyArray)\r
- {\r
+ public void setProperty(\r
+ final jalview.schemabinding.version2.Property[] vPropertyArray) {\r
//-- copy array\r
- _propertyList.removeAllElements();\r
- for (int i = 0; i < propertyArray.length; i++) {\r
- _propertyList.addElement(propertyArray[i]);\r
+ _propertyList.clear();\r
+ \r
+ for (int i = 0; i < vPropertyArray.length; i++) {\r
+ this._propertyList.add(vPropertyArray[i]);\r
}\r
- } //-- void setProperty(jalview.schemabinding.version2.Property) \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Pdbids.\r
//--------------------------/\r
\r
/**\r
- * Field _structureStateList\r
+ * Field _structureStateList.\r
*/\r
private java.util.Vector _structureStateList;\r
\r
\r
public Pdbids() {\r
super();\r
- _structureStateList = new Vector();\r
- } //-- jalview.schemabinding.version2.Pdbids()\r
+ this._structureStateList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addStructureState\r
- * \r
* \r
* \r
* @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addStructureState(jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _structureStateList.addElement(vStructureState);\r
- } //-- void addStructureState(jalview.schemabinding.version2.StructureState) \r
+ public void addStructureState(\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._structureStateList.addElement(vStructureState);\r
+ }\r
\r
/**\r
- * Method addStructureState\r
- * \r
* \r
* \r
* @param index\r
* @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _structureStateList.insertElementAt(vStructureState, index);\r
- } //-- void addStructureState(int, jalview.schemabinding.version2.StructureState) \r
+ public void addStructureState(\r
+ final int index,\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._structureStateList.add(index, vStructureState);\r
+ }\r
\r
/**\r
- * Method enumerateStructureState\r
- * \r
- * \r
+ * Method enumerateStructureState.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.StructureState elements\r
*/\r
- public java.util.Enumeration enumerateStructureState()\r
- {\r
- return _structureStateList.elements();\r
- } //-- java.util.Enumeration enumerateStructureState() \r
+ public java.util.Enumeration enumerateStructureState(\r
+ ) {\r
+ return this._structureStateList.elements();\r
+ }\r
\r
/**\r
- * Method getStructureState\r
- * \r
- * \r
+ * Method getStructureState.\r
* \r
* @param index\r
- * @return StructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.StructureState at the given\r
+ * index\r
*/\r
- public jalview.schemabinding.version2.StructureState getStructureState(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _structureStateList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.StructureState getStructureState(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.StructureState getStructureState(int) \r
+ return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);\r
+ }\r
\r
/**\r
- * Method getStructureState\r
- * \r
- * \r
- * \r
- * @return StructureState\r
+ * Method getStructureState.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.StructureState[] getStructureState()\r
- {\r
- int size = _structureStateList.size();\r
- jalview.schemabinding.version2.StructureState[] mArray = new jalview.schemabinding.version2.StructureState[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.StructureState[] getStructureState() \r
+ public jalview.schemabinding.version2.StructureState[] getStructureState(\r
+ ) {\r
+ jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];\r
+ return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getStructureStateCount\r
- * \r
- * \r
+ * Method getStructureStateCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getStructureStateCount()\r
- {\r
- return _structureStateList.size();\r
- } //-- int getStructureStateCount() \r
+ public int getStructureStateCount(\r
+ ) {\r
+ return this._structureStateList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllStructureState\r
- * \r
*/\r
- public void removeAllStructureState()\r
- {\r
- _structureStateList.removeAllElements();\r
- } //-- void removeAllStructureState() \r
+ public void removeAllStructureState(\r
+ ) {\r
+ this._structureStateList.clear();\r
+ }\r
\r
/**\r
- * Method removeStructureState\r
- * \r
+ * Method removeStructureState.\r
* \r
+ * @param vStructureState\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeStructureState(\r
+ final jalview.schemabinding.version2.StructureState vStructureState) {\r
+ boolean removed = _structureStateList.remove(vStructureState);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeStructureStateAt.\r
* \r
* @param index\r
- * @return StructureState\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.StructureState removeStructureState(int index)\r
- {\r
- java.lang.Object obj = _structureStateList.elementAt(index);\r
- _structureStateList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.StructureState removeStructureStateAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._structureStateList.remove(index);\r
return (jalview.schemabinding.version2.StructureState) obj;\r
- } //-- jalview.schemabinding.version2.StructureState removeStructureState(int) \r
+ }\r
\r
/**\r
- * Method setStructureState\r
- * \r
* \r
* \r
* @param index\r
* @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _structureStateList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setStructureState(\r
+ final int index,\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
}\r
- _structureStateList.setElementAt(vStructureState, index);\r
- } //-- void setStructureState(int, jalview.schemabinding.version2.StructureState) \r
+ \r
+ this._structureStateList.set(index, vStructureState);\r
+ }\r
\r
/**\r
- * Method setStructureState\r
- * \r
* \r
* \r
- * @param structureStateArray\r
+ * @param vStructureStateArray\r
*/\r
- public void setStructureState(jalview.schemabinding.version2.StructureState[] structureStateArray)\r
- {\r
+ public void setStructureState(\r
+ final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {\r
//-- copy array\r
- _structureStateList.removeAllElements();\r
- for (int i = 0; i < structureStateArray.length; i++) {\r
- _structureStateList.addElement(structureStateArray[i]);\r
+ _structureStateList.clear();\r
+ \r
+ for (int i = 0; i < vStructureStateArray.length; i++) {\r
+ this._structureStateList.add(vStructureStateArray[i]);\r
}\r
- } //-- void setStructureState(jalview.schemabinding.version2.StructureState) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Pdbentry\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Property.\r
//--------------------------/\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
/**\r
- * Field _value\r
+ * Field _value.\r
*/\r
private java.lang.String _value;\r
\r
\r
public Property() {\r
super();\r
- } //-- jalview.schemabinding.version2.Property()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'name'.\r
* \r
- * @return String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
* Returns the value of field 'value'.\r
* \r
- * @return String\r
- * @return the value of field 'value'.\r
+ * @return the value of field 'Value'.\r
*/\r
- public java.lang.String getValue()\r
- {\r
+ public java.lang.String getValue(\r
+ ) {\r
return this._value;\r
- } //-- java.lang.String getValue() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'value'.\r
* \r
* @param value the value of field 'value'.\r
*/\r
- public void setValue(java.lang.String value)\r
- {\r
+ public void setValue(\r
+ final java.lang.String value) {\r
this._value = value;\r
- } //-- void setValue(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Property\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.Property unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Sequence.\r
//--------------------------/\r
\r
/**\r
- * Field _DBRefList\r
+ * Field _DBRefList.\r
*/\r
private java.util.Vector _DBRefList;\r
\r
\r
public Sequence() {\r
super();\r
- _DBRefList = new Vector();\r
- } //-- jalview.schemabinding.version2.Sequence()\r
+ this._DBRefList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addDBRef\r
- * \r
* \r
* \r
* @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.addElement(vDBRef);\r
- } //-- void addDBRef(jalview.schemabinding.version2.DBRef) \r
+ public void addDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.addElement(vDBRef);\r
+ }\r
\r
/**\r
- * Method addDBRef\r
- * \r
* \r
* \r
* @param index\r
* @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.insertElementAt(vDBRef, index);\r
- } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) \r
+ public void addDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.add(index, vDBRef);\r
+ }\r
\r
/**\r
- * Method enumerateDBRef\r
- * \r
- * \r
+ * Method enumerateDBRef.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.DBRef elements\r
*/\r
- public java.util.Enumeration enumerateDBRef()\r
- {\r
- return _DBRefList.elements();\r
- } //-- java.util.Enumeration enumerateDBRef() \r
+ public java.util.Enumeration enumerateDBRef(\r
+ ) {\r
+ return this._DBRefList.elements();\r
+ }\r
\r
/**\r
- * Method getDBRef\r
- * \r
- * \r
+ * Method getDBRef.\r
* \r
* @param index\r
- * @return DBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.DBRef at the given index\r
*/\r
- public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _DBRefList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.DBRef getDBRef(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.DBRef getDBRef(int) \r
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);\r
+ }\r
\r
/**\r
- * Method getDBRef\r
- * \r
- * \r
+ * Method getDBRef.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return DBRef\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.DBRef[] getDBRef()\r
- {\r
- int size = _DBRefList.size();\r
- jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.DBRef[] getDBRef() \r
+ public jalview.schemabinding.version2.DBRef[] getDBRef(\r
+ ) {\r
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];\r
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getDBRefCount\r
- * \r
+ * Method getDBRefCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getDBRefCount()\r
- {\r
- return _DBRefList.size();\r
- } //-- int getDBRefCount() \r
+ public int getDBRefCount(\r
+ ) {\r
+ return this._DBRefList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllDBRef\r
- * \r
*/\r
- public void removeAllDBRef()\r
- {\r
- _DBRefList.removeAllElements();\r
- } //-- void removeAllDBRef() \r
+ public void removeAllDBRef(\r
+ ) {\r
+ this._DBRefList.clear();\r
+ }\r
\r
/**\r
- * Method removeDBRef\r
- * \r
+ * Method removeDBRef.\r
* \r
+ * @param vDBRef\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef) {\r
+ boolean removed = _DBRefList.remove(vDBRef);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeDBRefAt.\r
* \r
* @param index\r
- * @return DBRef\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
- {\r
- java.lang.Object obj = _DBRefList.elementAt(index);\r
- _DBRefList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._DBRefList.remove(index);\r
return (jalview.schemabinding.version2.DBRef) obj;\r
- } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) \r
+ }\r
\r
/**\r
- * Method setDBRef\r
- * \r
* \r
* \r
* @param index\r
* @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _DBRefList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
}\r
- _DBRefList.setElementAt(vDBRef, index);\r
- } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) \r
+ \r
+ this._DBRefList.set(index, vDBRef);\r
+ }\r
\r
/**\r
- * Method setDBRef\r
* \r
* \r
- * \r
- * @param DBRefArray\r
+ * @param vDBRefArray\r
*/\r
- public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
- {\r
+ public void setDBRef(\r
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray) {\r
//-- copy array\r
- _DBRefList.removeAllElements();\r
- for (int i = 0; i < DBRefArray.length; i++) {\r
- _DBRefList.addElement(DBRefArray[i]);\r
+ _DBRefList.clear();\r
+ \r
+ for (int i = 0; i < vDBRefArray.length; i++) {\r
+ this._DBRefList.add(vDBRefArray[i]);\r
}\r
- } //-- void setDBRef(jalview.schemabinding.version2.DBRef) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.SequenceType\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ public static jalview.schemabinding.version2.SequenceType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class SequenceSet.\r
//--------------------------/\r
\r
/**\r
- * Field _gapChar\r
+ * Field _gapChar.\r
*/\r
private java.lang.String _gapChar;\r
\r
/**\r
- * Field _sequenceList\r
+ * Field _sequenceList.\r
*/\r
private java.util.Vector _sequenceList;\r
\r
/**\r
- * Field _annotationList\r
+ * Field _annotationList.\r
*/\r
private java.util.Vector _annotationList;\r
\r
/**\r
- * Field _sequenceSetPropertiesList\r
+ * Field _sequenceSetPropertiesList.\r
*/\r
private java.util.Vector _sequenceSetPropertiesList;\r
\r
\r
public SequenceSet() {\r
super();\r
- _sequenceList = new Vector();\r
- _annotationList = new Vector();\r
- _sequenceSetPropertiesList = new Vector();\r
- } //-- jalview.schemabinding.version2.SequenceSet()\r
+ this._sequenceList = new java.util.Vector();\r
+ this._annotationList = new java.util.Vector();\r
+ this._sequenceSetPropertiesList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addAnnotation\r
- * \r
* \r
* \r
* @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) \r
+ public void addAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationList.addElement(vAnnotation);\r
+ }\r
\r
/**\r
- * Method addAnnotation\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) \r
+ public void addAnnotation(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationList.add(index, vAnnotation);\r
+ }\r
\r
/**\r
- * Method addSequence\r
- * \r
* \r
* \r
* @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.schemabinding.version2.Sequence) \r
+ public void addSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceList.addElement(vSequence);\r
+ }\r
\r
/**\r
- * Method addSequence\r
- * \r
* \r
* \r
* @param index\r
* @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) \r
+ public void addSequence(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceList.add(index, vSequence);\r
+ }\r
\r
/**\r
- * Method addSequenceSetProperties\r
- * \r
* \r
* \r
* @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
- } //-- void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) \r
+ public void addSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
+ }\r
\r
/**\r
- * Method addSequenceSetProperties\r
- * \r
* \r
* \r
* @param index\r
* @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetPropertiesList.insertElementAt(vSequenceSetProperties, index);\r
- } //-- void addSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) \r
+ public void addSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);\r
+ }\r
\r
/**\r
- * Method enumerateAnnotation\r
- * \r
- * \r
+ * Method enumerateAnnotation.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Annotation elements\r
*/\r
- public java.util.Enumeration enumerateAnnotation()\r
- {\r
- return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation() \r
+ public java.util.Enumeration enumerateAnnotation(\r
+ ) {\r
+ return this._annotationList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateSequence\r
- * \r
- * \r
+ * Method enumerateSequence.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Sequence elements\r
*/\r
- public java.util.Enumeration enumerateSequence()\r
- {\r
- return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence() \r
+ public java.util.Enumeration enumerateSequence(\r
+ ) {\r
+ return this._sequenceList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateSequenceSetProperties\r
+ * Method enumerateSequenceSetProperties.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSetProperties elements\r
*/\r
- public java.util.Enumeration enumerateSequenceSetProperties()\r
- {\r
- return _sequenceSetPropertiesList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSetProperties() \r
+ public java.util.Enumeration enumerateSequenceSetProperties(\r
+ ) {\r
+ return this._sequenceSetPropertiesList.elements();\r
+ }\r
\r
/**\r
- * Method getAnnotation\r
- * \r
- * \r
+ * Method getAnnotation.\r
* \r
* @param index\r
- * @return Annotation\r
- */\r
- public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Annotation at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Annotation getAnnotation(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) \r
+ return (jalview.schemabinding.version2.Annotation) _annotationList.get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotation\r
- * \r
+ * Method getAnnotation.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * @return Annotation\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
- {\r
- int size = _annotationList.size();\r
- jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() \r
+ public jalview.schemabinding.version2.Annotation[] getAnnotation(\r
+ ) {\r
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];\r
+ return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getAnnotationCount\r
- * \r
+ * Method getAnnotationCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getAnnotationCount()\r
- {\r
- return _annotationList.size();\r
- } //-- int getAnnotationCount() \r
+ public int getAnnotationCount(\r
+ ) {\r
+ return this._annotationList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'gapChar'.\r
* \r
- * @return String\r
- * @return the value of field 'gapChar'.\r
+ * @return the value of field 'GapChar'.\r
*/\r
- public java.lang.String getGapChar()\r
- {\r
+ public java.lang.String getGapChar(\r
+ ) {\r
return this._gapChar;\r
- } //-- java.lang.String getGapChar() \r
+ }\r
\r
/**\r
- * Method getSequence\r
- * \r
- * \r
+ * Method getSequence.\r
* \r
* @param index\r
- * @return Sequence\r
- */\r
- public jalview.schemabinding.version2.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Sequence at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Sequence getSequence(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Sequence getSequence(int) \r
+ return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index);\r
+ }\r
\r
/**\r
- * Method getSequence\r
- * \r
- * \r
+ * Method getSequence.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return Sequence\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Sequence[] getSequence()\r
- {\r
- int size = _sequenceList.size();\r
- jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Sequence[] getSequence() \r
+ public jalview.schemabinding.version2.Sequence[] getSequence(\r
+ ) {\r
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];\r
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getSequenceCount\r
- * \r
+ * Method getSequenceCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSequenceCount()\r
- {\r
- return _sequenceList.size();\r
- } //-- int getSequenceCount() \r
+ public int getSequenceCount(\r
+ ) {\r
+ return this._sequenceList.size();\r
+ }\r
\r
/**\r
- * Method getSequenceSetProperties\r
- * \r
- * \r
+ * Method getSequenceSetProperties.\r
* \r
* @param index\r
- * @return SequenceSetProperties\r
- */\r
- public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.SequenceSetProperties at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int) \r
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);\r
+ }\r
\r
/**\r
- * Method getSequenceSetProperties\r
- * \r
- * \r
+ * Method getSequenceSetProperties.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
* \r
- * @return SequenceSetProperties\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()\r
- {\r
- int size = _sequenceSetPropertiesList.size();\r
- jalview.schemabinding.version2.SequenceSetProperties[] mArray = new jalview.schemabinding.version2.SequenceSetProperties[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() \r
+ public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(\r
+ ) {\r
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];\r
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getSequenceSetPropertiesCount\r
- * \r
- * \r
+ * Method getSequenceSetPropertiesCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSequenceSetPropertiesCount()\r
- {\r
- return _sequenceSetPropertiesList.size();\r
- } //-- int getSequenceSetPropertiesCount() \r
+ public int getSequenceSetPropertiesCount(\r
+ ) {\r
+ return this._sequenceSetPropertiesList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
- * \r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllAnnotation\r
- * \r
*/\r
- public void removeAllAnnotation()\r
- {\r
- _annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation() \r
+ public void removeAllAnnotation(\r
+ ) {\r
+ this._annotationList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllSequence\r
- * \r
*/\r
- public void removeAllSequence()\r
- {\r
- _sequenceList.removeAllElements();\r
- } //-- void removeAllSequence() \r
+ public void removeAllSequence(\r
+ ) {\r
+ this._sequenceList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllSequenceSetProperties\r
- * \r
*/\r
- public void removeAllSequenceSetProperties()\r
- {\r
- _sequenceSetPropertiesList.removeAllElements();\r
- } //-- void removeAllSequenceSetProperties() \r
+ public void removeAllSequenceSetProperties(\r
+ ) {\r
+ this._sequenceSetPropertiesList.clear();\r
+ }\r
\r
/**\r
- * Method removeAnnotation\r
- * \r
+ * Method removeAnnotation.\r
* \r
+ * @param vAnnotation\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation) {\r
+ boolean removed = _annotationList.remove(vAnnotation);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationAt.\r
* \r
* @param index\r
- * @return Annotation\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Annotation removeAnnotation(int index)\r
- {\r
- java.lang.Object obj = _annotationList.elementAt(index);\r
- _annotationList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationList.remove(index);\r
return (jalview.schemabinding.version2.Annotation) obj;\r
- } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int) \r
+ }\r
\r
/**\r
- * Method removeSequence\r
- * \r
+ * Method removeSequence.\r
* \r
+ * @param vSequence\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence) {\r
+ boolean removed = _sequenceList.remove(vSequence);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceAt.\r
* \r
* @param index\r
- * @return Sequence\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Sequence removeSequence(int index)\r
- {\r
- java.lang.Object obj = _sequenceList.elementAt(index);\r
- _sequenceList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceList.remove(index);\r
return (jalview.schemabinding.version2.Sequence) obj;\r
- } //-- jalview.schemabinding.version2.Sequence removeSequence(int) \r
+ }\r
\r
/**\r
- * Method removeSequenceSetProperties\r
- * \r
+ * Method removeSequenceSetProperties.\r
* \r
+ * @param vSequenceSetProperties\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {\r
+ boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetPropertiesAt.\r
* \r
* @param index\r
- * @return SequenceSetProperties\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetPropertiesList.elementAt(index);\r
- _sequenceSetPropertiesList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);\r
return (jalview.schemabinding.version2.SequenceSetProperties) obj;\r
- } //-- jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int) \r
+ }\r
\r
/**\r
- * Method setAnnotation\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotation\r
- */\r
- public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotation(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");\r
}\r
- _annotationList.setElementAt(vAnnotation, index);\r
- } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation) \r
+ \r
+ this._annotationList.set(index, vAnnotation);\r
+ }\r
\r
/**\r
- * Method setAnnotation\r
* \r
* \r
- * \r
- * @param annotationArray\r
+ * @param vAnnotationArray\r
*/\r
- public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)\r
- {\r
+ public void setAnnotation(\r
+ final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {\r
//-- copy array\r
- _annotationList.removeAllElements();\r
- for (int i = 0; i < annotationArray.length; i++) {\r
- _annotationList.addElement(annotationArray[i]);\r
+ _annotationList.clear();\r
+ \r
+ for (int i = 0; i < vAnnotationArray.length; i++) {\r
+ this._annotationList.add(vAnnotationArray[i]);\r
}\r
- } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) \r
+ }\r
\r
/**\r
* Sets the value of field 'gapChar'.\r
* \r
* @param gapChar the value of field 'gapChar'.\r
*/\r
- public void setGapChar(java.lang.String gapChar)\r
- {\r
+ public void setGapChar(\r
+ final java.lang.String gapChar) {\r
this._gapChar = gapChar;\r
- } //-- void setGapChar(java.lang.String) \r
+ }\r
\r
/**\r
- * Method setSequence\r
- * \r
* \r
* \r
* @param index\r
* @param vSequence\r
- */\r
- public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSequence(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");\r
}\r
- _sequenceList.setElementAt(vSequence, index);\r
- } //-- void setSequence(int, jalview.schemabinding.version2.Sequence) \r
+ \r
+ this._sequenceList.set(index, vSequence);\r
+ }\r
\r
/**\r
- * Method setSequence\r
* \r
* \r
- * \r
- * @param sequenceArray\r
+ * @param vSequenceArray\r
*/\r
- public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)\r
- {\r
+ public void setSequence(\r
+ final jalview.schemabinding.version2.Sequence[] vSequenceArray) {\r
//-- copy array\r
- _sequenceList.removeAllElements();\r
- for (int i = 0; i < sequenceArray.length; i++) {\r
- _sequenceList.addElement(sequenceArray[i]);\r
+ _sequenceList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceArray.length; i++) {\r
+ this._sequenceList.add(vSequenceArray[i]);\r
}\r
- } //-- void setSequence(jalview.schemabinding.version2.Sequence) \r
+ }\r
\r
/**\r
- * Method setSequenceSetProperties\r
- * \r
* \r
* \r
* @param index\r
* @param vSequenceSetProperties\r
- */\r
- public void setSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
}\r
- _sequenceSetPropertiesList.setElementAt(vSequenceSetProperties, index);\r
- } //-- void setSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) \r
+ \r
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);\r
+ }\r
\r
/**\r
- * Method setSequenceSetProperties\r
* \r
* \r
- * \r
- * @param sequenceSetPropertiesArray\r
+ * @param vSequenceSetPropertiesArray\r
*/\r
- public void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties[] sequenceSetPropertiesArray)\r
- {\r
+ public void setSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {\r
//-- copy array\r
- _sequenceSetPropertiesList.removeAllElements();\r
- for (int i = 0; i < sequenceSetPropertiesArray.length; i++) {\r
- _sequenceSetPropertiesList.addElement(sequenceSetPropertiesArray[i]);\r
+ _sequenceSetPropertiesList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {\r
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);\r
}\r
- } //-- void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.SequenceSet\r
+ */\r
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class SequenceSetProperties.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SequenceSetProperties implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _key\r
- */\r
- private java.lang.String _key;\r
-\r
- /**\r
- * Field _value\r
- */\r
- private java.lang.String _value;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceSetProperties() {\r
- super();\r
- } //-- jalview.schemabinding.version2.SequenceSetProperties()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'key'.\r
- * \r
- * @return String\r
- * @return the value of field 'key'.\r
- */\r
- public java.lang.String getKey()\r
- {\r
- return this._key;\r
- } //-- java.lang.String getKey() \r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return String\r
- * @return the value of field 'value'.\r
- */\r
- public java.lang.String getValue()\r
- {\r
- return this._value;\r
- } //-- java.lang.String getValue() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'key'.\r
- * \r
- * @param key the value of field 'key'.\r
- */\r
- public void setKey(java.lang.String key)\r
- {\r
- this._key = key;\r
- } //-- void setKey(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value the value of field 'value'.\r
- */\r
- public void setValue(java.lang.String value)\r
- {\r
- this._value = value;\r
- } //-- void setValue(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+/*
+ * 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 -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequenceSetProperties.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceSetProperties implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _key.
+ */
+ private java.lang.String _key;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSetProperties() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'key'.
+ *
+ * @return the value of field 'Key'.
+ */
+ public java.lang.String getKey(
+ ) {
+ return this._key;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'key'.
+ *
+ * @param key the value of field 'key'.
+ */
+ public void setKey(
+ final java.lang.String key) {
+ this._key = key;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final java.lang.String value) {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.SequenceSetProperties
+ */
+ public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class SequenceType.\r
//--------------------------/\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private java.lang.String _id;\r
\r
/**\r
- * Field _description\r
+ * Field _description.\r
*/\r
private java.lang.String _description;\r
\r
/**\r
- * Field _sequence\r
+ * Field _sequence.\r
*/\r
private java.lang.String _sequence;\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
\r
public SequenceType() {\r
super();\r
- } //-- jalview.schemabinding.version2.SequenceType()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'description'.\r
* \r
- * @return String\r
- * @return the value of field 'description'.\r
+ * @return the value of field 'Description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription(\r
+ ) {\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ }\r
\r
/**\r
* Returns the value of field 'id'.\r
* \r
- * @return String\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId(\r
+ ) {\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ }\r
\r
/**\r
* Returns the value of field 'name'.\r
* \r
- * @return String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
* Returns the value of field 'sequence'.\r
* \r
- * @return String\r
- * @return the value of field 'sequence'.\r
+ * @return the value of field 'Sequence'.\r
*/\r
- public java.lang.String getSequence()\r
- {\r
+ public java.lang.String getSequence(\r
+ ) {\r
return this._sequence;\r
- } //-- java.lang.String getSequence() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'description'.\r
* \r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(\r
+ final java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'sequence'.\r
* \r
* @param sequence the value of field 'sequence'.\r
*/\r
- public void setSequence(java.lang.String sequence)\r
- {\r
+ public void setSequence(\r
+ final java.lang.String sequence) {\r
this._sequence = sequence;\r
- } //-- void setSequence(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.SequenceType\r
+ */\r
+ public static jalview.schemabinding.version2.SequenceType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Setting.\r
//--------------------------/\r
\r
/**\r
- * Field _type\r
+ * Field _type.\r
*/\r
private java.lang.String _type;\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private int _colour;\r
\r
private boolean _has_colour;\r
\r
/**\r
- * Field _display\r
+ * Field _display.\r
*/\r
private boolean _display;\r
\r
private boolean _has_display;\r
\r
/**\r
- * Field _order\r
+ * Field _order.\r
*/\r
private float _order;\r
\r
\r
public Setting() {\r
super();\r
- } //-- jalview.schemabinding.version2.Setting()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteColour\r
- * \r
*/\r
- public void deleteColour()\r
- {\r
+ public void deleteColour(\r
+ ) {\r
this._has_colour= false;\r
- } //-- void deleteColour() \r
+ }\r
\r
/**\r
- * Method deleteDisplay\r
- * \r
*/\r
- public void deleteDisplay()\r
- {\r
+ public void deleteDisplay(\r
+ ) {\r
this._has_display= false;\r
- } //-- void deleteDisplay() \r
+ }\r
\r
/**\r
- * Method deleteOrder\r
- * \r
*/\r
- public void deleteOrder()\r
- {\r
+ public void deleteOrder(\r
+ ) {\r
this._has_order= false;\r
- } //-- void deleteOrder() \r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return int\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public int getColour()\r
- {\r
+ public int getColour(\r
+ ) {\r
return this._colour;\r
- } //-- int getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'display'.\r
* \r
- * @return boolean\r
- * @return the value of field 'display'.\r
+ * @return the value of field 'Display'.\r
*/\r
- public boolean getDisplay()\r
- {\r
+ public boolean getDisplay(\r
+ ) {\r
return this._display;\r
- } //-- boolean getDisplay() \r
+ }\r
\r
/**\r
* Returns the value of field 'order'.\r
* \r
- * @return float\r
- * @return the value of field 'order'.\r
+ * @return the value of field 'Order'.\r
*/\r
- public float getOrder()\r
- {\r
+ public float getOrder(\r
+ ) {\r
return this._order;\r
- } //-- float getOrder() \r
+ }\r
\r
/**\r
* Returns the value of field 'type'.\r
* \r
- * @return String\r
- * @return the value of field 'type'.\r
+ * @return the value of field 'Type'.\r
*/\r
- public java.lang.String getType()\r
- {\r
+ public java.lang.String getType(\r
+ ) {\r
return this._type;\r
- } //-- java.lang.String getType() \r
+ }\r
\r
/**\r
- * Method hasColour\r
+ * Method hasColour.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Colour has been added\r
*/\r
- public boolean hasColour()\r
- {\r
+ public boolean hasColour(\r
+ ) {\r
return this._has_colour;\r
- } //-- boolean hasColour() \r
+ }\r
\r
/**\r
- * Method hasDisplay\r
- * \r
+ * Method hasDisplay.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Display has been added\r
*/\r
- public boolean hasDisplay()\r
- {\r
+ public boolean hasDisplay(\r
+ ) {\r
return this._has_display;\r
- } //-- boolean hasDisplay() \r
+ }\r
\r
/**\r
- * Method hasOrder\r
- * \r
- * \r
+ * Method hasOrder.\r
* \r
- * @return boolean\r
+ * @return true if at least one Order has been added\r
*/\r
- public boolean hasOrder()\r
- {\r
+ public boolean hasOrder(\r
+ ) {\r
return this._has_order;\r
- } //-- boolean hasOrder() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Returns the value of field 'display'.\r
* \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean isDisplay(\r
+ ) {\r
+ return this._display;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(int colour)\r
- {\r
+ public void setColour(\r
+ final int colour) {\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'display'.\r
* \r
* @param display the value of field 'display'.\r
*/\r
- public void setDisplay(boolean display)\r
- {\r
+ public void setDisplay(\r
+ final boolean display) {\r
this._display = display;\r
this._has_display = true;\r
- } //-- void setDisplay(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'order'.\r
* \r
* @param order the value of field 'order'.\r
*/\r
- public void setOrder(float order)\r
- {\r
+ public void setOrder(\r
+ final float order) {\r
this._order = order;\r
this._has_order = true;\r
- } //-- void setOrder(float) \r
+ }\r
\r
/**\r
* Sets the value of field 'type'.\r
* \r
* @param type the value of field 'type'.\r
*/\r
- public void setType(java.lang.String type)\r
- {\r
+ public void setType(\r
+ final java.lang.String type) {\r
this._type = type;\r
- } //-- void setType(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Settin\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.Setting unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
* Schema.
* $Id$
*/
//- Imported classes and packages -/
//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
* Class StructureState.
private java.lang.String _content = "";
/**
- * Field _visible
+ * Field _visible.
*/
private boolean _visible;
private boolean _has_visible;
/**
- * Field _xpos
+ * Field _xpos.
*/
private int _xpos;
private boolean _has_xpos;
/**
- * Field _ypos
+ * Field _ypos.
*/
private int _ypos;
private boolean _has_ypos;
/**
- * Field _width
+ * Field _width.
*/
private int _width;
private boolean _has_width;
/**
- * Field _height
+ * Field _height.
*/
private int _height;
public StructureState() {
super();
setContent("");
- } //-- jalview.schemabinding.version2.StructureState()
+ }
//-----------/
//-----------/
/**
- * Method deleteHeight
- *
*/
- public void deleteHeight()
- {
+ public void deleteHeight(
+ ) {
this._has_height= false;
- } //-- void deleteHeight()
+ }
/**
- * Method deleteVisible
- *
*/
- public void deleteVisible()
- {
+ public void deleteVisible(
+ ) {
this._has_visible= false;
- } //-- void deleteVisible()
+ }
/**
- * Method deleteWidth
- *
*/
- public void deleteWidth()
- {
+ public void deleteWidth(
+ ) {
this._has_width= false;
- } //-- void deleteWidth()
+ }
/**
- * Method deleteXpos
- *
*/
- public void deleteXpos()
- {
+ public void deleteXpos(
+ ) {
this._has_xpos= false;
- } //-- void deleteXpos()
+ }
/**
- * Method deleteYpos
- *
*/
- public void deleteYpos()
- {
+ public void deleteYpos(
+ ) {
this._has_ypos= false;
- } //-- void deleteYpos()
+ }
/**
* Returns the value of field 'content'. The field 'content'
* has the following description: internal content storage
*
- * @return String
- * @return the value of field 'content'.
+ * @return the value of field 'Content'.
*/
- public java.lang.String getContent()
- {
+ public java.lang.String getContent(
+ ) {
return this._content;
- } //-- java.lang.String getContent()
+ }
/**
* Returns the value of field 'height'.
*
- * @return int
- * @return the value of field 'height'.
+ * @return the value of field 'Height'.
*/
- public int getHeight()
- {
+ public int getHeight(
+ ) {
return this._height;
- } //-- int getHeight()
+ }
/**
* Returns the value of field 'visible'.
*
- * @return boolean
- * @return the value of field 'visible'.
+ * @return the value of field 'Visible'.
*/
- public boolean getVisible()
- {
+ public boolean getVisible(
+ ) {
return this._visible;
- } //-- boolean getVisible()
+ }
/**
* Returns the value of field 'width'.
*
- * @return int
- * @return the value of field 'width'.
+ * @return the value of field 'Width'.
*/
- public int getWidth()
- {
+ public int getWidth(
+ ) {
return this._width;
- } //-- int getWidth()
+ }
/**
* Returns the value of field 'xpos'.
*
- * @return int
- * @return the value of field 'xpos'.
+ * @return the value of field 'Xpos'.
*/
- public int getXpos()
- {
+ public int getXpos(
+ ) {
return this._xpos;
- } //-- int getXpos()
+ }
/**
* Returns the value of field 'ypos'.
*
- * @return int
- * @return the value of field 'ypos'.
+ * @return the value of field 'Ypos'.
*/
- public int getYpos()
- {
+ public int getYpos(
+ ) {
return this._ypos;
- } //-- int getYpos()
+ }
/**
- * Method hasHeight
- *
+ * Method hasHeight.
*
- *
- * @return boolean
+ * @return true if at least one Height has been added
*/
- public boolean hasHeight()
- {
+ public boolean hasHeight(
+ ) {
return this._has_height;
- } //-- boolean hasHeight()
+ }
/**
- * Method hasVisible
- *
+ * Method hasVisible.
*
- *
- * @return boolean
+ * @return true if at least one Visible has been added
*/
- public boolean hasVisible()
- {
+ public boolean hasVisible(
+ ) {
return this._has_visible;
- } //-- boolean hasVisible()
+ }
/**
- * Method hasWidth
- *
+ * Method hasWidth.
*
- *
- * @return boolean
+ * @return true if at least one Width has been added
*/
- public boolean hasWidth()
- {
+ public boolean hasWidth(
+ ) {
return this._has_width;
- } //-- boolean hasWidth()
+ }
/**
- * Method hasXpos
- *
+ * Method hasXpos.
*
- *
- * @return boolean
+ * @return true if at least one Xpos has been added
*/
- public boolean hasXpos()
- {
+ public boolean hasXpos(
+ ) {
return this._has_xpos;
- } //-- boolean hasXpos()
+ }
/**
- * Method hasYpos
- *
- *
+ * Method hasYpos.
*
- * @return boolean
+ * @return true if at least one Ypos has been added
*/
- public boolean hasYpos()
- {
+ public boolean hasYpos(
+ ) {
return this._has_ypos;
- } //-- boolean hasYpos()
+ }
/**
- * Method isValid
+ * Method isValid.
*
- *
- *
- * @return boolean
+ * @return true if this object is valid according to the schema
*/
- public boolean isValid()
- {
+ public boolean isValid(
+ ) {
try {
validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ } catch (org.exolab.castor.xml.ValidationException vex) {
return false;
}
return true;
- } //-- boolean isValid()
+ }
/**
- * Method marshal
+ * Returns the value of field 'visible'.
*
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible(
+ ) {
+ return this._visible;
+ }
+
+ /**
*
*
* @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or 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);
- } //-- void marshal(java.io.Writer)
+ }
/**
- * Method marshal
- *
*
*
* @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ * @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);
- } //-- void marshal(org.xml.sax.ContentHandler)
+ }
/**
* Sets the value of field 'content'. The field 'content' has
*
* @param content the value of field 'content'.
*/
- public void setContent(java.lang.String content)
- {
+ public void setContent(
+ final java.lang.String content) {
this._content = content;
- } //-- void setContent(java.lang.String)
+ }
/**
* Sets the value of field 'height'.
*
* @param height the value of field 'height'.
*/
- public void setHeight(int height)
- {
+ public void setHeight(
+ final int height) {
this._height = height;
this._has_height = true;
- } //-- void setHeight(int)
+ }
/**
* Sets the value of field 'visible'.
*
* @param visible the value of field 'visible'.
*/
- public void setVisible(boolean visible)
- {
+ public void setVisible(
+ final boolean visible) {
this._visible = visible;
this._has_visible = true;
- } //-- void setVisible(boolean)
+ }
/**
* Sets the value of field 'width'.
*
* @param width the value of field 'width'.
*/
- public void setWidth(int width)
- {
+ public void setWidth(
+ final int width) {
this._width = width;
this._has_width = true;
- } //-- void setWidth(int)
+ }
/**
* Sets the value of field 'xpos'.
*
* @param xpos the value of field 'xpos'.
*/
- public void setXpos(int xpos)
- {
+ public void setXpos(
+ final int xpos) {
this._xpos = xpos;
this._has_xpos = true;
- } //-- void setXpos(int)
+ }
/**
* Sets the value of field 'ypos'.
*
* @param ypos the value of field 'ypos'.
*/
- public void setYpos(int ypos)
- {
+ public void setYpos(
+ final int ypos) {
this._ypos = ypos;
this._has_ypos = true;
- } //-- void setYpos(int)
+ }
/**
- * Method unmarshal
- *
- *
+ * Method unmarshal.
*
* @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.StructureState
+ */
+ public static jalview.schemabinding.version2.StructureState unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
- } //-- java.lang.Object unmarshal(java.io.Reader)
+ }
/**
- * Method validate
*
+ *
+ * @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
- {
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
validator.validate(this);
- } //-- void validate()
+ }
}
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class ThresholdLine.\r
//--------------------------/\r
\r
/**\r
- * Field _label\r
+ * Field _label.\r
*/\r
private java.lang.String _label;\r
\r
/**\r
- * Field _value\r
+ * Field _value.\r
*/\r
private float _value;\r
\r
private boolean _has_value;\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private int _colour;\r
\r
\r
public ThresholdLine() {\r
super();\r
- } //-- jalview.schemabinding.version2.ThresholdLine()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteColour\r
- * \r
*/\r
- public void deleteColour()\r
- {\r
+ public void deleteColour(\r
+ ) {\r
this._has_colour= false;\r
- } //-- void deleteColour() \r
+ }\r
\r
/**\r
- * Method deleteValue\r
- * \r
*/\r
- public void deleteValue()\r
- {\r
+ public void deleteValue(\r
+ ) {\r
this._has_value= false;\r
- } //-- void deleteValue() \r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return int\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public int getColour()\r
- {\r
+ public int getColour(\r
+ ) {\r
return this._colour;\r
- } //-- int getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'label'.\r
* \r
- * @return String\r
- * @return the value of field 'label'.\r
+ * @return the value of field 'Label'.\r
*/\r
- public java.lang.String getLabel()\r
- {\r
+ public java.lang.String getLabel(\r
+ ) {\r
return this._label;\r
- } //-- java.lang.String getLabel() \r
+ }\r
\r
/**\r
* Returns the value of field 'value'.\r
* \r
- * @return float\r
- * @return the value of field 'value'.\r
+ * @return the value of field 'Value'.\r
*/\r
- public float getValue()\r
- {\r
+ public float getValue(\r
+ ) {\r
return this._value;\r
- } //-- float getValue() \r
+ }\r
\r
/**\r
- * Method hasColour\r
- * \r
+ * Method hasColour.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Colour has been added\r
*/\r
- public boolean hasColour()\r
- {\r
+ public boolean hasColour(\r
+ ) {\r
return this._has_colour;\r
- } //-- boolean hasColour() \r
+ }\r
\r
/**\r
- * Method hasValue\r
- * \r
+ * Method hasValue.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Value has been added\r
*/\r
- public boolean hasValue()\r
- {\r
+ public boolean hasValue(\r
+ ) {\r
return this._has_value;\r
- } //-- boolean hasValue() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(int colour)\r
- {\r
+ public void setColour(\r
+ final int colour) {\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'label'.\r
* \r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label)\r
- {\r
+ public void setLabel(\r
+ final java.lang.String label) {\r
this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'value'.\r
* \r
* @param value the value of field 'value'.\r
*/\r
- public void setValue(float value)\r
- {\r
+ public void setValue(\r
+ final float value) {\r
this._value = value;\r
this._has_value = true;\r
- } //-- void setValue(float) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.ThresholdLine\r
+ */\r
+ public static jalview.schemabinding.version2.ThresholdLine unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Tree.\r
//--------------------------/\r
\r
/**\r
- * Field _width\r
+ * Field _width.\r
*/\r
private int _width;\r
\r
private boolean _has_width;\r
\r
/**\r
- * Field _height\r
+ * Field _height.\r
*/\r
private int _height;\r
\r
private boolean _has_height;\r
\r
/**\r
- * Field _xpos\r
+ * Field _xpos.\r
*/\r
private int _xpos;\r
\r
private boolean _has_xpos;\r
\r
/**\r
- * Field _ypos\r
+ * Field _ypos.\r
*/\r
private int _ypos;\r
\r
private boolean _has_ypos;\r
\r
/**\r
- * Field _fontName\r
+ * Field _fontName.\r
*/\r
private java.lang.String _fontName;\r
\r
/**\r
- * Field _fontSize\r
+ * Field _fontSize.\r
*/\r
private int _fontSize;\r
\r
private boolean _has_fontSize;\r
\r
/**\r
- * Field _fontStyle\r
+ * Field _fontStyle.\r
*/\r
private int _fontStyle;\r
\r
private boolean _has_fontStyle;\r
\r
/**\r
- * Field _threshold\r
+ * Field _threshold.\r
*/\r
private float _threshold;\r
\r
private boolean _has_threshold;\r
\r
/**\r
- * Field _showBootstrap\r
+ * Field _showBootstrap.\r
*/\r
private boolean _showBootstrap;\r
\r
private boolean _has_showBootstrap;\r
\r
/**\r
- * Field _showDistances\r
+ * Field _showDistances.\r
*/\r
private boolean _showDistances;\r
\r
private boolean _has_showDistances;\r
\r
/**\r
- * Field _markUnlinked\r
+ * Field _markUnlinked.\r
*/\r
private boolean _markUnlinked;\r
\r
private boolean _has_markUnlinked;\r
\r
/**\r
- * Field _fitToWindow\r
+ * Field _fitToWindow.\r
*/\r
private boolean _fitToWindow;\r
\r
private boolean _has_fitToWindow;\r
\r
/**\r
- * Field _currentTree\r
+ * Field _currentTree.\r
*/\r
private boolean _currentTree;\r
\r
private boolean _has_currentTree;\r
\r
/**\r
- * Field _title\r
+ * Field _title.\r
*/\r
private java.lang.String _title;\r
\r
/**\r
- * Field _newick\r
+ * Field _newick.\r
*/\r
private java.lang.String _newick;\r
\r
\r
public Tree() {\r
super();\r
- } //-- jalview.schemabinding.version2.Tree()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method deleteCurrentTree\r
- * \r
*/\r
- public void deleteCurrentTree()\r
- {\r
+ public void deleteCurrentTree(\r
+ ) {\r
this._has_currentTree= false;\r
- } //-- void deleteCurrentTree() \r
+ }\r
\r
/**\r
- * Method deleteFitToWindow\r
- * \r
*/\r
- public void deleteFitToWindow()\r
- {\r
+ public void deleteFitToWindow(\r
+ ) {\r
this._has_fitToWindow= false;\r
- } //-- void deleteFitToWindow() \r
+ }\r
\r
/**\r
- * Method deleteFontSize\r
- * \r
*/\r
- public void deleteFontSize()\r
- {\r
+ public void deleteFontSize(\r
+ ) {\r
this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
+ }\r
\r
/**\r
- * Method deleteFontStyle\r
- * \r
*/\r
- public void deleteFontStyle()\r
- {\r
+ public void deleteFontStyle(\r
+ ) {\r
this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
+ }\r
\r
/**\r
- * Method deleteHeight\r
- * \r
*/\r
- public void deleteHeight()\r
- {\r
+ public void deleteHeight(\r
+ ) {\r
this._has_height= false;\r
- } //-- void deleteHeight() \r
+ }\r
\r
/**\r
- * Method deleteMarkUnlinked\r
- * \r
*/\r
- public void deleteMarkUnlinked()\r
- {\r
+ public void deleteMarkUnlinked(\r
+ ) {\r
this._has_markUnlinked= false;\r
- } //-- void deleteMarkUnlinked() \r
+ }\r
\r
/**\r
- * Method deleteShowBootstrap\r
- * \r
*/\r
- public void deleteShowBootstrap()\r
- {\r
+ public void deleteShowBootstrap(\r
+ ) {\r
this._has_showBootstrap= false;\r
- } //-- void deleteShowBootstrap() \r
+ }\r
\r
/**\r
- * Method deleteShowDistances\r
- * \r
*/\r
- public void deleteShowDistances()\r
- {\r
+ public void deleteShowDistances(\r
+ ) {\r
this._has_showDistances= false;\r
- } //-- void deleteShowDistances() \r
+ }\r
\r
/**\r
- * Method deleteThreshold\r
- * \r
*/\r
- public void deleteThreshold()\r
- {\r
+ public void deleteThreshold(\r
+ ) {\r
this._has_threshold= false;\r
- } //-- void deleteThreshold() \r
+ }\r
\r
/**\r
- * Method deleteWidth\r
- * \r
*/\r
- public void deleteWidth()\r
- {\r
+ public void deleteWidth(\r
+ ) {\r
this._has_width= false;\r
- } //-- void deleteWidth() \r
+ }\r
\r
/**\r
- * Method deleteXpos\r
- * \r
*/\r
- public void deleteXpos()\r
- {\r
+ public void deleteXpos(\r
+ ) {\r
this._has_xpos= false;\r
- } //-- void deleteXpos() \r
+ }\r
\r
/**\r
- * Method deleteYpos\r
- * \r
*/\r
- public void deleteYpos()\r
- {\r
+ public void deleteYpos(\r
+ ) {\r
this._has_ypos= false;\r
- } //-- void deleteYpos() \r
+ }\r
\r
/**\r
* Returns the value of field 'currentTree'.\r
* \r
- * @return boolean\r
- * @return the value of field 'currentTree'.\r
+ * @return the value of field 'CurrentTree'.\r
*/\r
- public boolean getCurrentTree()\r
- {\r
+ public boolean getCurrentTree(\r
+ ) {\r
return this._currentTree;\r
- } //-- boolean getCurrentTree() \r
+ }\r
\r
/**\r
* Returns the value of field 'fitToWindow'.\r
* \r
- * @return boolean\r
- * @return the value of field 'fitToWindow'.\r
+ * @return the value of field 'FitToWindow'.\r
*/\r
- public boolean getFitToWindow()\r
- {\r
+ public boolean getFitToWindow(\r
+ ) {\r
return this._fitToWindow;\r
- } //-- boolean getFitToWindow() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontName'.\r
* \r
- * @return String\r
- * @return the value of field 'fontName'.\r
+ * @return the value of field 'FontName'.\r
*/\r
- public java.lang.String getFontName()\r
- {\r
+ public java.lang.String getFontName(\r
+ ) {\r
return this._fontName;\r
- } //-- java.lang.String getFontName() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontSize'.\r
* \r
- * @return int\r
- * @return the value of field 'fontSize'.\r
+ * @return the value of field 'FontSize'.\r
*/\r
- public int getFontSize()\r
- {\r
+ public int getFontSize(\r
+ ) {\r
return this._fontSize;\r
- } //-- int getFontSize() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontStyle'.\r
* \r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
+ * @return the value of field 'FontStyle'.\r
*/\r
- public int getFontStyle()\r
- {\r
+ public int getFontStyle(\r
+ ) {\r
return this._fontStyle;\r
- } //-- int getFontStyle() \r
+ }\r
\r
/**\r
* Returns the value of field 'height'.\r
* \r
- * @return int\r
- * @return the value of field 'height'.\r
+ * @return the value of field 'Height'.\r
*/\r
- public int getHeight()\r
- {\r
+ public int getHeight(\r
+ ) {\r
return this._height;\r
- } //-- int getHeight() \r
+ }\r
\r
/**\r
* Returns the value of field 'markUnlinked'.\r
* \r
- * @return boolean\r
- * @return the value of field 'markUnlinked'.\r
+ * @return the value of field 'MarkUnlinked'.\r
*/\r
- public boolean getMarkUnlinked()\r
- {\r
+ public boolean getMarkUnlinked(\r
+ ) {\r
return this._markUnlinked;\r
- } //-- boolean getMarkUnlinked() \r
+ }\r
\r
/**\r
* Returns the value of field 'newick'.\r
* \r
- * @return String\r
- * @return the value of field 'newick'.\r
+ * @return the value of field 'Newick'.\r
*/\r
- public java.lang.String getNewick()\r
- {\r
+ public java.lang.String getNewick(\r
+ ) {\r
return this._newick;\r
- } //-- java.lang.String getNewick() \r
+ }\r
\r
/**\r
* Returns the value of field 'showBootstrap'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showBootstrap'.\r
+ * @return the value of field 'ShowBootstrap'.\r
*/\r
- public boolean getShowBootstrap()\r
- {\r
+ public boolean getShowBootstrap(\r
+ ) {\r
return this._showBootstrap;\r
- } //-- boolean getShowBootstrap() \r
+ }\r
\r
/**\r
* Returns the value of field 'showDistances'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showDistances'.\r
+ * @return the value of field 'ShowDistances'.\r
*/\r
- public boolean getShowDistances()\r
- {\r
+ public boolean getShowDistances(\r
+ ) {\r
return this._showDistances;\r
- } //-- boolean getShowDistances() \r
+ }\r
\r
/**\r
* Returns the value of field 'threshold'.\r
* \r
- * @return float\r
- * @return the value of field 'threshold'.\r
+ * @return the value of field 'Threshold'.\r
*/\r
- public float getThreshold()\r
- {\r
+ public float getThreshold(\r
+ ) {\r
return this._threshold;\r
- } //-- float getThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'title'.\r
* \r
- * @return String\r
- * @return the value of field 'title'.\r
+ * @return the value of field 'Title'.\r
*/\r
- public java.lang.String getTitle()\r
- {\r
+ public java.lang.String getTitle(\r
+ ) {\r
return this._title;\r
- } //-- java.lang.String getTitle() \r
+ }\r
\r
/**\r
* Returns the value of field 'width'.\r
* \r
- * @return int\r
- * @return the value of field 'width'.\r
+ * @return the value of field 'Width'.\r
*/\r
- public int getWidth()\r
- {\r
+ public int getWidth(\r
+ ) {\r
return this._width;\r
- } //-- int getWidth() \r
+ }\r
\r
/**\r
* Returns the value of field 'xpos'.\r
* \r
- * @return int\r
- * @return the value of field 'xpos'.\r
+ * @return the value of field 'Xpos'.\r
*/\r
- public int getXpos()\r
- {\r
+ public int getXpos(\r
+ ) {\r
return this._xpos;\r
- } //-- int getXpos() \r
+ }\r
\r
/**\r
* Returns the value of field 'ypos'.\r
* \r
- * @return int\r
- * @return the value of field 'ypos'.\r
+ * @return the value of field 'Ypos'.\r
*/\r
- public int getYpos()\r
- {\r
+ public int getYpos(\r
+ ) {\r
return this._ypos;\r
- } //-- int getYpos() \r
+ }\r
\r
/**\r
- * Method hasCurrentTree\r
- * \r
- * \r
+ * Method hasCurrentTree.\r
* \r
- * @return boolean\r
+ * @return true if at least one CurrentTree has been added\r
*/\r
- public boolean hasCurrentTree()\r
- {\r
+ public boolean hasCurrentTree(\r
+ ) {\r
return this._has_currentTree;\r
- } //-- boolean hasCurrentTree() \r
+ }\r
\r
/**\r
- * Method hasFitToWindow\r
+ * Method hasFitToWindow.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one FitToWindow has been added\r
*/\r
- public boolean hasFitToWindow()\r
- {\r
+ public boolean hasFitToWindow(\r
+ ) {\r
return this._has_fitToWindow;\r
- } //-- boolean hasFitToWindow() \r
+ }\r
\r
/**\r
- * Method hasFontSize\r
- * \r
- * \r
+ * Method hasFontSize.\r
* \r
- * @return boolean\r
+ * @return true if at least one FontSize has been added\r
*/\r
- public boolean hasFontSize()\r
- {\r
+ public boolean hasFontSize(\r
+ ) {\r
return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
+ }\r
\r
/**\r
- * Method hasFontStyle\r
+ * Method hasFontStyle.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one FontStyle has been added\r
*/\r
- public boolean hasFontStyle()\r
- {\r
+ public boolean hasFontStyle(\r
+ ) {\r
return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
+ }\r
\r
/**\r
- * Method hasHeight\r
- * \r
+ * Method hasHeight.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one Height has been added\r
*/\r
- public boolean hasHeight()\r
- {\r
+ public boolean hasHeight(\r
+ ) {\r
return this._has_height;\r
- } //-- boolean hasHeight() \r
+ }\r
\r
/**\r
- * Method hasMarkUnlinked\r
- * \r
+ * Method hasMarkUnlinked.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one MarkUnlinked has been added\r
*/\r
- public boolean hasMarkUnlinked()\r
- {\r
+ public boolean hasMarkUnlinked(\r
+ ) {\r
return this._has_markUnlinked;\r
- } //-- boolean hasMarkUnlinked() \r
+ }\r
\r
/**\r
- * Method hasShowBootstrap\r
- * \r
+ * Method hasShowBootstrap.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowBootstrap has been added\r
*/\r
- public boolean hasShowBootstrap()\r
- {\r
+ public boolean hasShowBootstrap(\r
+ ) {\r
return this._has_showBootstrap;\r
- } //-- boolean hasShowBootstrap() \r
+ }\r
\r
/**\r
- * Method hasShowDistances\r
- * \r
+ * Method hasShowDistances.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowDistances has been added\r
*/\r
- public boolean hasShowDistances()\r
- {\r
+ public boolean hasShowDistances(\r
+ ) {\r
return this._has_showDistances;\r
- } //-- boolean hasShowDistances() \r
+ }\r
\r
/**\r
- * Method hasThreshold\r
- * \r
- * \r
+ * Method hasThreshold.\r
* \r
- * @return boolean\r
+ * @return true if at least one Threshold has been added\r
*/\r
- public boolean hasThreshold()\r
- {\r
+ public boolean hasThreshold(\r
+ ) {\r
return this._has_threshold;\r
- } //-- boolean hasThreshold() \r
+ }\r
\r
/**\r
- * Method hasWidth\r
- * \r
- * \r
+ * Method hasWidth.\r
* \r
- * @return boolean\r
+ * @return true if at least one Width has been added\r
*/\r
- public boolean hasWidth()\r
- {\r
+ public boolean hasWidth(\r
+ ) {\r
return this._has_width;\r
- } //-- boolean hasWidth() \r
+ }\r
\r
/**\r
- * Method hasXpos\r
+ * Method hasXpos.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Xpos has been added\r
*/\r
- public boolean hasXpos()\r
- {\r
+ public boolean hasXpos(\r
+ ) {\r
return this._has_xpos;\r
- } //-- boolean hasXpos() \r
+ }\r
\r
/**\r
- * Method hasYpos\r
+ * Method hasYpos.\r
* \r
+ * @return true if at least one Ypos has been added\r
+ */\r
+ public boolean hasYpos(\r
+ ) {\r
+ return this._has_ypos;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'currentTree'.\r
* \r
+ * @return the value of field 'CurrentTree'.\r
+ */\r
+ public boolean isCurrentTree(\r
+ ) {\r
+ return this._currentTree;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'FitToWindow'.\r
*/\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \r
+ public boolean isFitToWindow(\r
+ ) {\r
+ return this._fitToWindow;\r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Returns the value of field 'markUnlinked'.\r
* \r
+ * @return the value of field 'MarkUnlinked'.\r
+ */\r
+ public boolean isMarkUnlinked(\r
+ ) {\r
+ return this._markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
* \r
+ * @return the value of field 'ShowBootstrap'.\r
+ */\r
+ public boolean isShowBootstrap(\r
+ ) {\r
+ return this._showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'ShowDistances'.\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isShowDistances(\r
+ ) {\r
+ return this._showDistances;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'currentTree'.\r
* \r
* @param currentTree the value of field 'currentTree'.\r
*/\r
- public void setCurrentTree(boolean currentTree)\r
- {\r
+ public void setCurrentTree(\r
+ final boolean currentTree) {\r
this._currentTree = currentTree;\r
this._has_currentTree = true;\r
- } //-- void setCurrentTree(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'fitToWindow'.\r
* \r
* @param fitToWindow the value of field 'fitToWindow'.\r
*/\r
- public void setFitToWindow(boolean fitToWindow)\r
- {\r
+ public void setFitToWindow(\r
+ final boolean fitToWindow) {\r
this._fitToWindow = fitToWindow;\r
this._has_fitToWindow = true;\r
- } //-- void setFitToWindow(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontName'.\r
* \r
* @param fontName the value of field 'fontName'.\r
*/\r
- public void setFontName(java.lang.String fontName)\r
- {\r
+ public void setFontName(\r
+ final java.lang.String fontName) {\r
this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontSize'.\r
* \r
* @param fontSize the value of field 'fontSize'.\r
*/\r
- public void setFontSize(int fontSize)\r
- {\r
+ public void setFontSize(\r
+ final int fontSize) {\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontStyle'.\r
* \r
* @param fontStyle the value of field 'fontStyle'.\r
*/\r
- public void setFontStyle(int fontStyle)\r
- {\r
+ public void setFontStyle(\r
+ final int fontStyle) {\r
this._fontStyle = fontStyle;\r
this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'height'.\r
* \r
* @param height the value of field 'height'.\r
*/\r
- public void setHeight(int height)\r
- {\r
+ public void setHeight(\r
+ final int height) {\r
this._height = height;\r
this._has_height = true;\r
- } //-- void setHeight(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'markUnlinked'.\r
* \r
* @param markUnlinked the value of field 'markUnlinked'.\r
*/\r
- public void setMarkUnlinked(boolean markUnlinked)\r
- {\r
+ public void setMarkUnlinked(\r
+ final boolean markUnlinked) {\r
this._markUnlinked = markUnlinked;\r
this._has_markUnlinked = true;\r
- } //-- void setMarkUnlinked(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'newick'.\r
* \r
* @param newick the value of field 'newick'.\r
*/\r
- public void setNewick(java.lang.String newick)\r
- {\r
+ public void setNewick(\r
+ final java.lang.String newick) {\r
this._newick = newick;\r
- } //-- void setNewick(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'showBootstrap'.\r
* \r
* @param showBootstrap the value of field 'showBootstrap'.\r
*/\r
- public void setShowBootstrap(boolean showBootstrap)\r
- {\r
+ public void setShowBootstrap(\r
+ final boolean showBootstrap) {\r
this._showBootstrap = showBootstrap;\r
this._has_showBootstrap = true;\r
- } //-- void setShowBootstrap(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showDistances'.\r
* \r
* @param showDistances the value of field 'showDistances'.\r
*/\r
- public void setShowDistances(boolean showDistances)\r
- {\r
+ public void setShowDistances(\r
+ final boolean showDistances) {\r
this._showDistances = showDistances;\r
this._has_showDistances = true;\r
- } //-- void setShowDistances(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'threshold'.\r
* \r
* @param threshold the value of field 'threshold'.\r
*/\r
- public void setThreshold(float threshold)\r
- {\r
+ public void setThreshold(\r
+ final float threshold) {\r
this._threshold = threshold;\r
this._has_threshold = true;\r
- } //-- void setThreshold(float) \r
+ }\r
\r
/**\r
* Sets the value of field 'title'.\r
* \r
* @param title the value of field 'title'.\r
*/\r
- public void setTitle(java.lang.String title)\r
- {\r
+ public void setTitle(\r
+ final java.lang.String title) {\r
this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'width'.\r
* \r
* @param width the value of field 'width'.\r
*/\r
- public void setWidth(int width)\r
- {\r
+ public void setWidth(\r
+ final int width) {\r
this._width = width;\r
this._has_width = true;\r
- } //-- void setWidth(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'xpos'.\r
* \r
* @param xpos the value of field 'xpos'.\r
*/\r
- public void setXpos(int xpos)\r
- {\r
+ public void setXpos(\r
+ final int xpos) {\r
this._xpos = xpos;\r
this._has_xpos = true;\r
- } //-- void setXpos(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'ypos'.\r
* \r
* @param ypos the value of field 'ypos'.\r
*/\r
- public void setYpos(int ypos)\r
- {\r
+ public void setYpos(\r
+ final int ypos) {\r
this._ypos = ypos;\r
this._has_ypos = true;\r
- } //-- void setYpos(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Tree\r
+ */\r
+ public static jalview.schemabinding.version2.Tree unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class UserColourScheme.\r
\r
public UserColourScheme() {\r
super();\r
- } //-- jalview.schemabinding.version2.UserColourScheme()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.JalviewUserColours\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class UserColours.\r
//--------------------------/\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private java.lang.String _id;\r
\r
/**\r
- * Field _userColourScheme\r
+ * Field _userColourScheme.\r
*/\r
private jalview.schemabinding.version2.UserColourScheme _userColourScheme;\r
\r
\r
public UserColours() {\r
super();\r
- } //-- jalview.schemabinding.version2.UserColours()\r
+ }\r
\r
\r
//-----------/\r
/**\r
* Returns the value of field 'id'.\r
* \r
- * @return String\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId(\r
+ ) {\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ }\r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
* \r
- * @return UserColourScheme\r
- * @return the value of field 'userColourScheme'.\r
+ * @return the value of field 'UserColourScheme'.\r
*/\r
- public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()\r
- {\r
+ public jalview.schemabinding.version2.UserColourScheme getUserColourScheme(\r
+ ) {\r
return this._userColourScheme;\r
- } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(\r
+ final java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
* \r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
- public void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme userColourScheme)\r
- {\r
+ public void setUserColourScheme(\r
+ final jalview.schemabinding.version2.UserColourScheme userColourScheme) {\r
this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.UserColours\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.UserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class VAMSAS.\r
//--------------------------/\r
\r
/**\r
- * Field _treeList\r
+ * Field _treeList.\r
*/\r
private java.util.Vector _treeList;\r
\r
/**\r
- * Field _sequenceSetList\r
+ * Field _sequenceSetList.\r
*/\r
private java.util.Vector _sequenceSetList;\r
\r
\r
public VAMSAS() {\r
super();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.schemabinding.version2.VAMSAS()\r
+ this._treeList = new java.util.Vector();\r
+ this._sequenceSetList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addSequenceSet\r
- * \r
* \r
* \r
* @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
+ public void addSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetList.addElement(vSequenceSet);\r
+ }\r
\r
/**\r
- * Method addSequenceSet\r
- * \r
* \r
* \r
* @param index\r
* @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
+ public void addSequenceSet(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetList.add(index, vSequenceSet);\r
+ }\r
\r
/**\r
- * Method addTree\r
- * \r
* \r
* \r
* @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String) \r
+ public void addTree(\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.addElement(vTree);\r
+ }\r
\r
/**\r
- * Method addTree\r
- * \r
* \r
* \r
* @param index\r
* @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String) \r
+ public void addTree(\r
+ final int index,\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.add(index, vTree);\r
+ }\r
\r
/**\r
- * Method enumerateSequenceSet\r
+ * Method enumerateSequenceSet.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSet elements\r
*/\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet() \r
+ public java.util.Enumeration enumerateSequenceSet(\r
+ ) {\r
+ return this._sequenceSetList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateTree\r
- * \r
+ * Method enumerateTree.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all java.lang.String elements\r
*/\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
+ public java.util.Enumeration enumerateTree(\r
+ ) {\r
+ return this._treeList.elements();\r
+ }\r
\r
/**\r
- * Method getSequenceSet\r
- * \r
- * \r
+ * Method getSequenceSet.\r
* \r
* @param index\r
- * @return SequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.SequenceSet at the given index\r
*/\r
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) \r
+ return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);\r
+ }\r
\r
/**\r
- * Method getSequenceSet\r
+ * Method getSequenceSet.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return SequenceSet\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() \r
+ public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(\r
+ ) {\r
+ jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
+ return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getSequenceSetCount\r
+ * Method getSequenceSetCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSequenceSetCount()\r
- {\r
- return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount() \r
+ public int getSequenceSetCount(\r
+ ) {\r
+ return this._sequenceSetList.size();\r
+ }\r
\r
/**\r
- * Method getTree\r
- * \r
- * \r
+ * Method getTree.\r
* \r
* @param index\r
- * @return String\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the java.lang.String at the given index\r
*/\r
- public java.lang.String getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public java.lang.String getTree(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
\r
- return (String)_treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int) \r
+ return (java.lang.String) _treeList.get(index);\r
+ }\r
\r
/**\r
- * Method getTree\r
+ * Method getTree.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return String\r
+ * @return this collection as an Array\r
*/\r
- public java.lang.String[] getTree()\r
- {\r
- int size = _treeList.size();\r
- java.lang.String[] mArray = new java.lang.String[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (String)_treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- java.lang.String[] getTree() \r
+ public java.lang.String[] getTree(\r
+ ) {\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._treeList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getTreeCount\r
+ * Method getTreeCount.\r
* \r
- * \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount() \r
+ public int getTreeCount(\r
+ ) {\r
+ return this._treeList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Method isValid.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllSequenceSet\r
- * \r
*/\r
- public void removeAllSequenceSet()\r
- {\r
- _sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet() \r
+ public void removeAllSequenceSet(\r
+ ) {\r
+ this._sequenceSetList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllTree\r
- * \r
*/\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
+ public void removeAllTree(\r
+ ) {\r
+ this._treeList.clear();\r
+ }\r
\r
/**\r
- * Method removeSequenceSet\r
- * \r
+ * Method removeSequenceSet.\r
* \r
+ * @param vSequenceSet\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet) {\r
+ boolean removed = _sequenceSetList.remove(vSequenceSet);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetAt.\r
* \r
* @param index\r
- * @return SequenceSet\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetList.elementAt(index);\r
- _sequenceSetList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceSetList.remove(index);\r
return (jalview.schemabinding.version2.SequenceSet) obj;\r
- } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) \r
+ }\r
\r
/**\r
- * Method removeTree\r
- * \r
+ * Method removeTree.\r
* \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(\r
+ final java.lang.String vTree) {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
* \r
* @param index\r
- * @return String\r
+ * @return the element removed from the collection\r
*/\r
- public java.lang.String removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (String)obj;\r
- } //-- java.lang.String removeTree(int) \r
+ public java.lang.String removeTreeAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
+ return (java.lang.String) obj;\r
+ }\r
\r
/**\r
- * Method setSequenceSet\r
- * \r
* \r
* \r
* @param index\r
* @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setSequenceSet(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
}\r
- _sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
+ \r
+ this._sequenceSetList.set(index, vSequenceSet);\r
+ }\r
\r
/**\r
- * Method setSequenceSet\r
* \r
* \r
- * \r
- * @param sequenceSetArray\r
+ * @param vSequenceSetArray\r
*/\r
- public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)\r
- {\r
+ public void setSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {\r
//-- copy array\r
- _sequenceSetList.removeAllElements();\r
- for (int i = 0; i < sequenceSetArray.length; i++) {\r
- _sequenceSetList.addElement(sequenceSetArray[i]);\r
+ _sequenceSetList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceSetArray.length; i++) {\r
+ this._sequenceSetList.add(vSequenceSetArray[i]);\r
}\r
- } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
+ }\r
\r
/**\r
- * Method setTree\r
- * \r
* \r
* \r
* @param index\r
* @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void setTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ public void setTree(\r
+ final int index,\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String) \r
+ \r
+ this._treeList.set(index, vTree);\r
+ }\r
\r
/**\r
- * Method setTree\r
- * \r
* \r
* \r
- * @param treeArray\r
+ * @param vTreeArray\r
*/\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
+ public void setTree(\r
+ final java.lang.String[] vTreeArray) {\r
//-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++) {\r
- _treeList.addElement(treeArray[i]);\r
+ _treeList.clear();\r
+ \r
+ for (int i = 0; i < vTreeArray.length; i++) {\r
+ this._treeList.add(vTreeArray[i]);\r
}\r
- } //-- void setTree(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class VamsasModel.\r
\r
public VamsasModel() {\r
super();\r
- } //-- jalview.schemabinding.version2.VamsasModel()\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method isValid\r
+ * Method isValid.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Viewport.\r
//--------------------------/\r
\r
/**\r
- * Field _conservationSelected\r
+ * Field _conservationSelected.\r
*/\r
private boolean _conservationSelected;\r
\r
private boolean _has_conservationSelected;\r
\r
/**\r
- * Field _pidSelected\r
+ * Field _pidSelected.\r
*/\r
private boolean _pidSelected;\r
\r
private boolean _has_pidSelected;\r
\r
/**\r
- * Field _bgColour\r
+ * Field _bgColour.\r
*/\r
private java.lang.String _bgColour;\r
\r
/**\r
- * Field _consThreshold\r
+ * Field _consThreshold.\r
*/\r
private int _consThreshold;\r
\r
private boolean _has_consThreshold;\r
\r
/**\r
- * Field _pidThreshold\r
+ * Field _pidThreshold.\r
*/\r
private int _pidThreshold;\r
\r
private boolean _has_pidThreshold;\r
\r
/**\r
- * Field _title\r
+ * Field _title.\r
*/\r
private java.lang.String _title;\r
\r
/**\r
- * Field _showFullId\r
+ * Field _showFullId.\r
*/\r
private boolean _showFullId;\r
\r
private boolean _has_showFullId;\r
\r
/**\r
- * Field _rightAlignIds\r
+ * Field _rightAlignIds.\r
*/\r
private boolean _rightAlignIds;\r
\r
private boolean _has_rightAlignIds;\r
\r
/**\r
- * Field _showText\r
+ * Field _showText.\r
*/\r
private boolean _showText;\r
\r
private boolean _has_showText;\r
\r
/**\r
- * Field _showColourText\r
+ * Field _showColourText.\r
*/\r
private boolean _showColourText;\r
\r
private boolean _has_showColourText;\r
\r
/**\r
- * Field _showBoxes\r
+ * Field _showBoxes.\r
*/\r
private boolean _showBoxes;\r
\r
private boolean _has_showBoxes;\r
\r
/**\r
- * Field _wrapAlignment\r
+ * Field _wrapAlignment.\r
*/\r
private boolean _wrapAlignment;\r
\r
private boolean _has_wrapAlignment;\r
\r
/**\r
- * Field _renderGaps\r
+ * Field _renderGaps.\r
*/\r
private boolean _renderGaps;\r
\r
private boolean _has_renderGaps;\r
\r
/**\r
- * Field _showSequenceFeatures\r
+ * Field _showSequenceFeatures.\r
*/\r
private boolean _showSequenceFeatures;\r
\r
private boolean _has_showSequenceFeatures;\r
\r
/**\r
- * Field _showAnnotation\r
+ * Field _showAnnotation.\r
*/\r
private boolean _showAnnotation;\r
\r
private boolean _has_showAnnotation;\r
\r
/**\r
- * Field _xpos\r
+ * Field _xpos.\r
*/\r
private int _xpos;\r
\r
private boolean _has_xpos;\r
\r
/**\r
- * Field _ypos\r
+ * Field _ypos.\r
*/\r
private int _ypos;\r
\r
private boolean _has_ypos;\r
\r
/**\r
- * Field _width\r
+ * Field _width.\r
*/\r
private int _width;\r
\r
private boolean _has_width;\r
\r
/**\r
- * Field _height\r
+ * Field _height.\r
*/\r
private int _height;\r
\r
private boolean _has_height;\r
\r
/**\r
- * Field _startRes\r
+ * Field _startRes.\r
*/\r
private int _startRes;\r
\r
private boolean _has_startRes;\r
\r
/**\r
- * Field _startSeq\r
+ * Field _startSeq.\r
*/\r
private int _startSeq;\r
\r
private boolean _has_startSeq;\r
\r
/**\r
- * Field _fontName\r
+ * Field _fontName.\r
*/\r
private java.lang.String _fontName;\r
\r
/**\r
- * Field _fontSize\r
+ * Field _fontSize.\r
*/\r
private int _fontSize;\r
\r
private boolean _has_fontSize;\r
\r
/**\r
- * Field _fontStyle\r
+ * Field _fontStyle.\r
*/\r
private int _fontStyle;\r
\r
private boolean _has_fontStyle;\r
\r
/**\r
- * Field _viewName\r
+ * Field _viewName.\r
*/\r
private java.lang.String _viewName;\r
\r
/**\r
- * Field _sequenceSetId\r
+ * Field _sequenceSetId.\r
*/\r
private java.lang.String _sequenceSetId;\r
\r
/**\r
- * Field _gatheredViews\r
+ * Field _gatheredViews.\r
*/\r
private boolean _gatheredViews;\r
\r
private boolean _has_gatheredViews;\r
\r
/**\r
- * Field _textCol1\r
+ * Field _textCol1.\r
*/\r
private int _textCol1;\r
\r
private boolean _has_textCol1;\r
\r
/**\r
- * Field _textCol2\r
+ * Field _textCol2.\r
*/\r
private int _textCol2;\r
\r
private boolean _has_textCol2;\r
\r
/**\r
- * Field _textColThreshold\r
+ * Field _textColThreshold.\r
*/\r
private int _textColThreshold;\r
\r
private boolean _has_textColThreshold;\r
\r
/**\r
- * Field _annotationColours\r
+ * Field _annotationColours.\r
*/\r
private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
\r
/**\r
- * Field _hiddenColumnsList\r
+ * Field _hiddenColumnsList.\r
*/\r
private java.util.Vector _hiddenColumnsList;\r
\r
\r
public Viewport() {\r
super();\r
- _hiddenColumnsList = new Vector();\r
- } //-- jalview.schemabinding.version2.Viewport()\r
+ this._hiddenColumnsList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addHiddenColumns\r
- * \r
* \r
* \r
* @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenColumnsList.addElement(vHiddenColumns);\r
- } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+ public void addHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenColumnsList.addElement(vHiddenColumns);\r
+ }\r
\r
/**\r
- * Method addHiddenColumns\r
- * \r
* \r
* \r
* @param index\r
* @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
- } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+ public void addHiddenColumns(\r
+ final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenColumnsList.add(index, vHiddenColumns);\r
+ }\r
\r
/**\r
- * Method deleteConsThreshold\r
- * \r
*/\r
- public void deleteConsThreshold()\r
- {\r
+ public void deleteConsThreshold(\r
+ ) {\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ }\r
\r
/**\r
- * Method deleteConservationSelected\r
- * \r
*/\r
- public void deleteConservationSelected()\r
- {\r
+ public void deleteConservationSelected(\r
+ ) {\r
this._has_conservationSelected= false;\r
- } //-- void deleteConservationSelected() \r
+ }\r
\r
/**\r
- * Method deleteFontSize\r
- * \r
*/\r
- public void deleteFontSize()\r
- {\r
+ public void deleteFontSize(\r
+ ) {\r
this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
+ }\r
\r
/**\r
- * Method deleteFontStyle\r
- * \r
*/\r
- public void deleteFontStyle()\r
- {\r
+ public void deleteFontStyle(\r
+ ) {\r
this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
+ }\r
\r
/**\r
- * Method deleteGatheredViews\r
- * \r
*/\r
- public void deleteGatheredViews()\r
- {\r
+ public void deleteGatheredViews(\r
+ ) {\r
this._has_gatheredViews= false;\r
- } //-- void deleteGatheredViews() \r
+ }\r
\r
/**\r
- * Method deleteHeight\r
- * \r
*/\r
- public void deleteHeight()\r
- {\r
+ public void deleteHeight(\r
+ ) {\r
this._has_height= false;\r
- } //-- void deleteHeight() \r
+ }\r
\r
/**\r
- * Method deletePidSelected\r
- * \r
*/\r
- public void deletePidSelected()\r
- {\r
+ public void deletePidSelected(\r
+ ) {\r
this._has_pidSelected= false;\r
- } //-- void deletePidSelected() \r
+ }\r
\r
/**\r
- * Method deletePidThreshold\r
- * \r
*/\r
- public void deletePidThreshold()\r
- {\r
+ public void deletePidThreshold(\r
+ ) {\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ }\r
\r
/**\r
- * Method deleteRenderGaps\r
- * \r
*/\r
- public void deleteRenderGaps()\r
- {\r
+ public void deleteRenderGaps(\r
+ ) {\r
this._has_renderGaps= false;\r
- } //-- void deleteRenderGaps() \r
+ }\r
\r
/**\r
- * Method deleteRightAlignIds\r
- * \r
*/\r
- public void deleteRightAlignIds()\r
- {\r
+ public void deleteRightAlignIds(\r
+ ) {\r
this._has_rightAlignIds= false;\r
- } //-- void deleteRightAlignIds() \r
+ }\r
\r
/**\r
- * Method deleteShowAnnotation\r
- * \r
*/\r
- public void deleteShowAnnotation()\r
- {\r
+ public void deleteShowAnnotation(\r
+ ) {\r
this._has_showAnnotation= false;\r
- } //-- void deleteShowAnnotation() \r
+ }\r
\r
/**\r
- * Method deleteShowBoxes\r
- * \r
*/\r
- public void deleteShowBoxes()\r
- {\r
+ public void deleteShowBoxes(\r
+ ) {\r
this._has_showBoxes= false;\r
- } //-- void deleteShowBoxes() \r
+ }\r
\r
/**\r
- * Method deleteShowColourText\r
- * \r
*/\r
- public void deleteShowColourText()\r
- {\r
+ public void deleteShowColourText(\r
+ ) {\r
this._has_showColourText= false;\r
- } //-- void deleteShowColourText() \r
+ }\r
\r
/**\r
- * Method deleteShowFullId\r
- * \r
*/\r
- public void deleteShowFullId()\r
- {\r
+ public void deleteShowFullId(\r
+ ) {\r
this._has_showFullId= false;\r
- } //-- void deleteShowFullId() \r
+ }\r
\r
/**\r
- * Method deleteShowSequenceFeatures\r
- * \r
*/\r
- public void deleteShowSequenceFeatures()\r
- {\r
+ public void deleteShowSequenceFeatures(\r
+ ) {\r
this._has_showSequenceFeatures= false;\r
- } //-- void deleteShowSequenceFeatures() \r
+ }\r
\r
/**\r
- * Method deleteShowText\r
- * \r
*/\r
- public void deleteShowText()\r
- {\r
+ public void deleteShowText(\r
+ ) {\r
this._has_showText= false;\r
- } //-- void deleteShowText() \r
+ }\r
\r
/**\r
- * Method deleteStartRes\r
- * \r
*/\r
- public void deleteStartRes()\r
- {\r
+ public void deleteStartRes(\r
+ ) {\r
this._has_startRes= false;\r
- } //-- void deleteStartRes() \r
+ }\r
\r
/**\r
- * Method deleteStartSeq\r
- * \r
*/\r
- public void deleteStartSeq()\r
- {\r
+ public void deleteStartSeq(\r
+ ) {\r
this._has_startSeq= false;\r
- } //-- void deleteStartSeq() \r
+ }\r
\r
/**\r
- * Method deleteTextCol1\r
- * \r
*/\r
- public void deleteTextCol1()\r
- {\r
+ public void deleteTextCol1(\r
+ ) {\r
this._has_textCol1= false;\r
- } //-- void deleteTextCol1() \r
+ }\r
\r
/**\r
- * Method deleteTextCol2\r
- * \r
*/\r
- public void deleteTextCol2()\r
- {\r
+ public void deleteTextCol2(\r
+ ) {\r
this._has_textCol2= false;\r
- } //-- void deleteTextCol2() \r
+ }\r
\r
/**\r
- * Method deleteTextColThreshold\r
- * \r
*/\r
- public void deleteTextColThreshold()\r
- {\r
+ public void deleteTextColThreshold(\r
+ ) {\r
this._has_textColThreshold= false;\r
- } //-- void deleteTextColThreshold() \r
+ }\r
\r
/**\r
- * Method deleteWidth\r
- * \r
*/\r
- public void deleteWidth()\r
- {\r
+ public void deleteWidth(\r
+ ) {\r
this._has_width= false;\r
- } //-- void deleteWidth() \r
+ }\r
\r
/**\r
- * Method deleteWrapAlignment\r
- * \r
*/\r
- public void deleteWrapAlignment()\r
- {\r
+ public void deleteWrapAlignment(\r
+ ) {\r
this._has_wrapAlignment= false;\r
- } //-- void deleteWrapAlignment() \r
+ }\r
\r
/**\r
- * Method deleteXpos\r
- * \r
*/\r
- public void deleteXpos()\r
- {\r
+ public void deleteXpos(\r
+ ) {\r
this._has_xpos= false;\r
- } //-- void deleteXpos() \r
+ }\r
\r
/**\r
- * Method deleteYpos\r
- * \r
*/\r
- public void deleteYpos()\r
- {\r
+ public void deleteYpos(\r
+ ) {\r
this._has_ypos= false;\r
- } //-- void deleteYpos() \r
+ }\r
\r
/**\r
- * Method enumerateHiddenColumns\r
+ * Method enumerateHiddenColumns.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.HiddenColumns elements\r
*/\r
- public java.util.Enumeration enumerateHiddenColumns()\r
- {\r
- return _hiddenColumnsList.elements();\r
- } //-- java.util.Enumeration enumerateHiddenColumns() \r
+ public java.util.Enumeration enumerateHiddenColumns(\r
+ ) {\r
+ return this._hiddenColumnsList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'annotationColours'.\r
* \r
- * @return AnnotationColours\r
- * @return the value of field 'annotationColours'.\r
+ * @return the value of field 'AnnotationColours'.\r
*/\r
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
- {\r
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(\r
+ ) {\r
return this._annotationColours;\r
- } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() \r
+ }\r
\r
/**\r
* Returns the value of field 'bgColour'.\r
* \r
- * @return String\r
- * @return the value of field 'bgColour'.\r
+ * @return the value of field 'BgColour'.\r
*/\r
- public java.lang.String getBgColour()\r
- {\r
+ public java.lang.String getBgColour(\r
+ ) {\r
return this._bgColour;\r
- } //-- java.lang.String getBgColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
+ * @return the value of field 'ConsThreshold'.\r
*/\r
- public int getConsThreshold()\r
- {\r
+ public int getConsThreshold(\r
+ ) {\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'conservationSelected'.\r
* \r
- * @return boolean\r
- * @return the value of field 'conservationSelected'.\r
+ * @return the value of field 'ConservationSelected'.\r
*/\r
- public boolean getConservationSelected()\r
- {\r
+ public boolean getConservationSelected(\r
+ ) {\r
return this._conservationSelected;\r
- } //-- boolean getConservationSelected() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontName'.\r
* \r
- * @return String\r
- * @return the value of field 'fontName'.\r
+ * @return the value of field 'FontName'.\r
*/\r
- public java.lang.String getFontName()\r
- {\r
+ public java.lang.String getFontName(\r
+ ) {\r
return this._fontName;\r
- } //-- java.lang.String getFontName() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontSize'.\r
* \r
- * @return int\r
- * @return the value of field 'fontSize'.\r
+ * @return the value of field 'FontSize'.\r
*/\r
- public int getFontSize()\r
- {\r
+ public int getFontSize(\r
+ ) {\r
return this._fontSize;\r
- } //-- int getFontSize() \r
+ }\r
\r
/**\r
* Returns the value of field 'fontStyle'.\r
* \r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
+ * @return the value of field 'FontStyle'.\r
*/\r
- public int getFontStyle()\r
- {\r
+ public int getFontStyle(\r
+ ) {\r
return this._fontStyle;\r
- } //-- int getFontStyle() \r
+ }\r
\r
/**\r
* Returns the value of field 'gatheredViews'.\r
* \r
- * @return boolean\r
- * @return the value of field 'gatheredViews'.\r
+ * @return the value of field 'GatheredViews'.\r
*/\r
- public boolean getGatheredViews()\r
- {\r
+ public boolean getGatheredViews(\r
+ ) {\r
return this._gatheredViews;\r
- } //-- boolean getGatheredViews() \r
+ }\r
\r
/**\r
* Returns the value of field 'height'.\r
* \r
- * @return int\r
- * @return the value of field 'height'.\r
+ * @return the value of field 'Height'.\r
*/\r
- public int getHeight()\r
- {\r
+ public int getHeight(\r
+ ) {\r
return this._height;\r
- } //-- int getHeight() \r
+ }\r
\r
/**\r
- * Method getHiddenColumns\r
- * \r
- * \r
+ * Method getHiddenColumns.\r
* \r
* @param index\r
- * @return HiddenColumns\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.HiddenColumns at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);\r
+ }\r
\r
/**\r
- * Method getHiddenColumns\r
- * \r
+ * Method getHiddenColumns.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
* \r
- * \r
- * @return HiddenColumns\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
- {\r
- int size = _hiddenColumnsList.size();\r
- jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(\r
+ ) {\r
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];\r
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getHiddenColumnsCount\r
- * \r
+ * Method getHiddenColumnsCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getHiddenColumnsCount()\r
- {\r
- return _hiddenColumnsList.size();\r
- } //-- int getHiddenColumnsCount() \r
+ public int getHiddenColumnsCount(\r
+ ) {\r
+ return this._hiddenColumnsList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'pidSelected'.\r
* \r
- * @return boolean\r
- * @return the value of field 'pidSelected'.\r
+ * @return the value of field 'PidSelected'.\r
*/\r
- public boolean getPidSelected()\r
- {\r
+ public boolean getPidSelected(\r
+ ) {\r
return this._pidSelected;\r
- } //-- boolean getPidSelected() \r
+ }\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
+ * @return the value of field 'PidThreshold'.\r
*/\r
- public int getPidThreshold()\r
- {\r
+ public int getPidThreshold(\r
+ ) {\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'renderGaps'.\r
* \r
- * @return boolean\r
- * @return the value of field 'renderGaps'.\r
+ * @return the value of field 'RenderGaps'.\r
*/\r
- public boolean getRenderGaps()\r
- {\r
+ public boolean getRenderGaps(\r
+ ) {\r
return this._renderGaps;\r
- } //-- boolean getRenderGaps() \r
+ }\r
\r
/**\r
* Returns the value of field 'rightAlignIds'.\r
* \r
- * @return boolean\r
- * @return the value of field 'rightAlignIds'.\r
+ * @return the value of field 'RightAlignIds'.\r
*/\r
- public boolean getRightAlignIds()\r
- {\r
+ public boolean getRightAlignIds(\r
+ ) {\r
return this._rightAlignIds;\r
- } //-- boolean getRightAlignIds() \r
+ }\r
\r
/**\r
* Returns the value of field 'sequenceSetId'.\r
* \r
- * @return String\r
- * @return the value of field 'sequenceSetId'.\r
+ * @return the value of field 'SequenceSetId'.\r
*/\r
- public java.lang.String getSequenceSetId()\r
- {\r
+ public java.lang.String getSequenceSetId(\r
+ ) {\r
return this._sequenceSetId;\r
- } //-- java.lang.String getSequenceSetId() \r
+ }\r
\r
/**\r
* Returns the value of field 'showAnnotation'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showAnnotation'.\r
+ * @return the value of field 'ShowAnnotation'.\r
*/\r
- public boolean getShowAnnotation()\r
- {\r
+ public boolean getShowAnnotation(\r
+ ) {\r
return this._showAnnotation;\r
- } //-- boolean getShowAnnotation() \r
+ }\r
\r
/**\r
* Returns the value of field 'showBoxes'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showBoxes'.\r
+ * @return the value of field 'ShowBoxes'.\r
*/\r
- public boolean getShowBoxes()\r
- {\r
+ public boolean getShowBoxes(\r
+ ) {\r
return this._showBoxes;\r
- } //-- boolean getShowBoxes() \r
+ }\r
\r
/**\r
* Returns the value of field 'showColourText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showColourText'.\r
+ * @return the value of field 'ShowColourText'.\r
*/\r
- public boolean getShowColourText()\r
- {\r
+ public boolean getShowColourText(\r
+ ) {\r
return this._showColourText;\r
- } //-- boolean getShowColourText() \r
+ }\r
\r
/**\r
* Returns the value of field 'showFullId'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showFullId'.\r
+ * @return the value of field 'ShowFullId'.\r
*/\r
- public boolean getShowFullId()\r
- {\r
+ public boolean getShowFullId(\r
+ ) {\r
return this._showFullId;\r
- } //-- boolean getShowFullId() \r
+ }\r
\r
/**\r
* Returns the value of field 'showSequenceFeatures'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showSequenceFeatures'.\r
+ * @return the value of field 'ShowSequenceFeatures'.\r
*/\r
- public boolean getShowSequenceFeatures()\r
- {\r
+ public boolean getShowSequenceFeatures(\r
+ ) {\r
return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures() \r
+ }\r
\r
/**\r
* Returns the value of field 'showText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'showText'.\r
+ * @return the value of field 'ShowText'.\r
*/\r
- public boolean getShowText()\r
- {\r
+ public boolean getShowText(\r
+ ) {\r
return this._showText;\r
- } //-- boolean getShowText() \r
+ }\r
\r
/**\r
* Returns the value of field 'startRes'.\r
* \r
- * @return int\r
- * @return the value of field 'startRes'.\r
+ * @return the value of field 'StartRes'.\r
*/\r
- public int getStartRes()\r
- {\r
+ public int getStartRes(\r
+ ) {\r
return this._startRes;\r
- } //-- int getStartRes() \r
+ }\r
\r
/**\r
* Returns the value of field 'startSeq'.\r
* \r
- * @return int\r
- * @return the value of field 'startSeq'.\r
+ * @return the value of field 'StartSeq'.\r
*/\r
- public int getStartSeq()\r
- {\r
+ public int getStartSeq(\r
+ ) {\r
return this._startSeq;\r
- } //-- int getStartSeq() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol1'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol1'.\r
+ * @return the value of field 'TextCol1'.\r
*/\r
- public int getTextCol1()\r
- {\r
+ public int getTextCol1(\r
+ ) {\r
return this._textCol1;\r
- } //-- int getTextCol1() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol2'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol2'.\r
+ * @return the value of field 'TextCol2'.\r
*/\r
- public int getTextCol2()\r
- {\r
+ public int getTextCol2(\r
+ ) {\r
return this._textCol2;\r
- } //-- int getTextCol2() \r
+ }\r
\r
/**\r
* Returns the value of field 'textColThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'textColThreshold'.\r
+ * @return the value of field 'TextColThreshold'.\r
*/\r
- public int getTextColThreshold()\r
- {\r
+ public int getTextColThreshold(\r
+ ) {\r
return this._textColThreshold;\r
- } //-- int getTextColThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'title'.\r
* \r
- * @return String\r
- * @return the value of field 'title'.\r
+ * @return the value of field 'Title'.\r
*/\r
- public java.lang.String getTitle()\r
- {\r
+ public java.lang.String getTitle(\r
+ ) {\r
return this._title;\r
- } //-- java.lang.String getTitle() \r
+ }\r
\r
/**\r
* Returns the value of field 'viewName'.\r
* \r
- * @return String\r
- * @return the value of field 'viewName'.\r
+ * @return the value of field 'ViewName'.\r
*/\r
- public java.lang.String getViewName()\r
- {\r
+ public java.lang.String getViewName(\r
+ ) {\r
return this._viewName;\r
- } //-- java.lang.String getViewName() \r
+ }\r
\r
/**\r
* Returns the value of field 'width'.\r
* \r
- * @return int\r
- * @return the value of field 'width'.\r
+ * @return the value of field 'Width'.\r
*/\r
- public int getWidth()\r
- {\r
+ public int getWidth(\r
+ ) {\r
return this._width;\r
- } //-- int getWidth() \r
+ }\r
\r
/**\r
* Returns the value of field 'wrapAlignment'.\r
* \r
- * @return boolean\r
- * @return the value of field 'wrapAlignment'.\r
+ * @return the value of field 'WrapAlignment'.\r
*/\r
- public boolean getWrapAlignment()\r
- {\r
+ public boolean getWrapAlignment(\r
+ ) {\r
return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment() \r
+ }\r
\r
/**\r
* Returns the value of field 'xpos'.\r
* \r
- * @return int\r
- * @return the value of field 'xpos'.\r
+ * @return the value of field 'Xpos'.\r
*/\r
- public int getXpos()\r
- {\r
+ public int getXpos(\r
+ ) {\r
return this._xpos;\r
- } //-- int getXpos() \r
+ }\r
\r
/**\r
* Returns the value of field 'ypos'.\r
* \r
- * @return int\r
- * @return the value of field 'ypos'.\r
+ * @return the value of field 'Ypos'.\r
*/\r
- public int getYpos()\r
- {\r
+ public int getYpos(\r
+ ) {\r
return this._ypos;\r
- } //-- int getYpos() \r
+ }\r
\r
/**\r
- * Method hasConsThreshold\r
- * \r
+ * Method hasConsThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ConsThreshold has been added\r
*/\r
- public boolean hasConsThreshold()\r
- {\r
+ public boolean hasConsThreshold(\r
+ ) {\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ }\r
\r
/**\r
- * Method hasConservationSelected\r
- * \r
- * \r
+ * Method hasConservationSelected.\r
* \r
- * @return boolean\r
+ * @return true if at least one ConservationSelected has been\r
+ * added\r
*/\r
- public boolean hasConservationSelected()\r
- {\r
+ public boolean hasConservationSelected(\r
+ ) {\r
return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected() \r
+ }\r
\r
/**\r
- * Method hasFontSize\r
- * \r
- * \r
+ * Method hasFontSize.\r
* \r
- * @return boolean\r
+ * @return true if at least one FontSize has been added\r
*/\r
- public boolean hasFontSize()\r
- {\r
+ public boolean hasFontSize(\r
+ ) {\r
return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
+ }\r
\r
/**\r
- * Method hasFontStyle\r
+ * Method hasFontStyle.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one FontStyle has been added\r
*/\r
- public boolean hasFontStyle()\r
- {\r
+ public boolean hasFontStyle(\r
+ ) {\r
return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
+ }\r
\r
/**\r
- * Method hasGatheredViews\r
- * \r
+ * Method hasGatheredViews.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one GatheredViews has been added\r
*/\r
- public boolean hasGatheredViews()\r
- {\r
+ public boolean hasGatheredViews(\r
+ ) {\r
return this._has_gatheredViews;\r
- } //-- boolean hasGatheredViews() \r
+ }\r
\r
/**\r
- * Method hasHeight\r
- * \r
- * \r
+ * Method hasHeight.\r
* \r
- * @return boolean\r
+ * @return true if at least one Height has been added\r
*/\r
- public boolean hasHeight()\r
- {\r
+ public boolean hasHeight(\r
+ ) {\r
return this._has_height;\r
- } //-- boolean hasHeight() \r
+ }\r
\r
/**\r
- * Method hasPidSelected\r
+ * Method hasPidSelected.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one PidSelected has been added\r
*/\r
- public boolean hasPidSelected()\r
- {\r
+ public boolean hasPidSelected(\r
+ ) {\r
return this._has_pidSelected;\r
- } //-- boolean hasPidSelected() \r
+ }\r
\r
/**\r
- * Method hasPidThreshold\r
- * \r
+ * Method hasPidThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one PidThreshold has been added\r
*/\r
- public boolean hasPidThreshold()\r
- {\r
+ public boolean hasPidThreshold(\r
+ ) {\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ }\r
\r
/**\r
- * Method hasRenderGaps\r
- * \r
+ * Method hasRenderGaps.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one RenderGaps has been added\r
*/\r
- public boolean hasRenderGaps()\r
- {\r
+ public boolean hasRenderGaps(\r
+ ) {\r
return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps() \r
+ }\r
\r
/**\r
- * Method hasRightAlignIds\r
- * \r
- * \r
+ * Method hasRightAlignIds.\r
* \r
- * @return boolean\r
+ * @return true if at least one RightAlignIds has been added\r
*/\r
- public boolean hasRightAlignIds()\r
- {\r
+ public boolean hasRightAlignIds(\r
+ ) {\r
return this._has_rightAlignIds;\r
- } //-- boolean hasRightAlignIds() \r
+ }\r
\r
/**\r
- * Method hasShowAnnotation\r
- * \r
- * \r
+ * Method hasShowAnnotation.\r
* \r
- * @return boolean\r
+ * @return true if at least one ShowAnnotation has been added\r
*/\r
- public boolean hasShowAnnotation()\r
- {\r
+ public boolean hasShowAnnotation(\r
+ ) {\r
return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation() \r
+ }\r
\r
/**\r
- * Method hasShowBoxes\r
+ * Method hasShowBoxes.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowBoxes has been added\r
*/\r
- public boolean hasShowBoxes()\r
- {\r
+ public boolean hasShowBoxes(\r
+ ) {\r
return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes() \r
+ }\r
\r
/**\r
- * Method hasShowColourText\r
- * \r
+ * Method hasShowColourText.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowColourText has been added\r
*/\r
- public boolean hasShowColourText()\r
- {\r
+ public boolean hasShowColourText(\r
+ ) {\r
return this._has_showColourText;\r
- } //-- boolean hasShowColourText() \r
+ }\r
\r
/**\r
- * Method hasShowFullId\r
- * \r
+ * Method hasShowFullId.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowFullId has been added\r
*/\r
- public boolean hasShowFullId()\r
- {\r
+ public boolean hasShowFullId(\r
+ ) {\r
return this._has_showFullId;\r
- } //-- boolean hasShowFullId() \r
+ }\r
\r
/**\r
- * Method hasShowSequenceFeatures\r
- * \r
- * \r
+ * Method hasShowSequenceFeatures.\r
* \r
- * @return boolean\r
+ * @return true if at least one ShowSequenceFeatures has been\r
+ * added\r
*/\r
- public boolean hasShowSequenceFeatures()\r
- {\r
+ public boolean hasShowSequenceFeatures(\r
+ ) {\r
return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures() \r
+ }\r
\r
/**\r
- * Method hasShowText\r
+ * Method hasShowText.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one ShowText has been added\r
*/\r
- public boolean hasShowText()\r
- {\r
+ public boolean hasShowText(\r
+ ) {\r
return this._has_showText;\r
- } //-- boolean hasShowText() \r
+ }\r
\r
/**\r
- * Method hasStartRes\r
- * \r
+ * Method hasStartRes.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one StartRes has been added\r
*/\r
- public boolean hasStartRes()\r
- {\r
+ public boolean hasStartRes(\r
+ ) {\r
return this._has_startRes;\r
- } //-- boolean hasStartRes() \r
+ }\r
\r
/**\r
- * Method hasStartSeq\r
- * \r
- * \r
+ * Method hasStartSeq.\r
* \r
- * @return boolean\r
+ * @return true if at least one StartSeq has been added\r
*/\r
- public boolean hasStartSeq()\r
- {\r
+ public boolean hasStartSeq(\r
+ ) {\r
return this._has_startSeq;\r
- } //-- boolean hasStartSeq() \r
+ }\r
\r
/**\r
- * Method hasTextCol1\r
- * \r
- * \r
+ * Method hasTextCol1.\r
* \r
- * @return boolean\r
+ * @return true if at least one TextCol1 has been added\r
*/\r
- public boolean hasTextCol1()\r
- {\r
+ public boolean hasTextCol1(\r
+ ) {\r
return this._has_textCol1;\r
- } //-- boolean hasTextCol1() \r
+ }\r
\r
/**\r
- * Method hasTextCol2\r
+ * Method hasTextCol2.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one TextCol2 has been added\r
*/\r
- public boolean hasTextCol2()\r
- {\r
+ public boolean hasTextCol2(\r
+ ) {\r
return this._has_textCol2;\r
- } //-- boolean hasTextCol2() \r
+ }\r
\r
/**\r
- * Method hasTextColThreshold\r
- * \r
+ * Method hasTextColThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one TextColThreshold has been added\r
*/\r
- public boolean hasTextColThreshold()\r
- {\r
+ public boolean hasTextColThreshold(\r
+ ) {\r
return this._has_textColThreshold;\r
- } //-- boolean hasTextColThreshold() \r
+ }\r
+\r
+ /**\r
+ * Method hasWidth.\r
+ * \r
+ * @return true if at least one Width has been added\r
+ */\r
+ public boolean hasWidth(\r
+ ) {\r
+ return this._has_width;\r
+ }\r
\r
/**\r
- * Method hasWidth\r
+ * Method hasWrapAlignment.\r
* \r
+ * @return true if at least one WrapAlignment has been added\r
+ */\r
+ public boolean hasWrapAlignment(\r
+ ) {\r
+ return this._has_wrapAlignment;\r
+ }\r
+\r
+ /**\r
+ * Method hasXpos.\r
* \r
+ * @return true if at least one Xpos has been added\r
+ */\r
+ public boolean hasXpos(\r
+ ) {\r
+ return this._has_xpos;\r
+ }\r
+\r
+ /**\r
+ * Method hasYpos.\r
* \r
- * @return boolean\r
+ * @return true if at least one Ypos has been added\r
*/\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
+ public boolean hasYpos(\r
+ ) {\r
+ return this._has_ypos;\r
+ }\r
\r
/**\r
- * Method hasWrapAlignment\r
+ * Returns the value of field 'conservationSelected'.\r
* \r
+ * @return the value of field 'ConservationSelected'.\r
+ */\r
+ public boolean isConservationSelected(\r
+ ) {\r
+ return this._conservationSelected;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'gatheredViews'.\r
* \r
+ * @return the value of field 'GatheredViews'.\r
+ */\r
+ public boolean isGatheredViews(\r
+ ) {\r
+ return this._gatheredViews;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidSelected'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'PidSelected'.\r
*/\r
- public boolean hasWrapAlignment()\r
- {\r
- return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment() \r
+ public boolean isPidSelected(\r
+ ) {\r
+ return this._pidSelected;\r
+ }\r
\r
/**\r
- * Method hasXpos\r
+ * Returns the value of field 'renderGaps'.\r
* \r
+ * @return the value of field 'RenderGaps'.\r
+ */\r
+ public boolean isRenderGaps(\r
+ ) {\r
+ return this._renderGaps;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'rightAlignIds'.\r
* \r
+ * @return the value of field 'RightAlignIds'.\r
+ */\r
+ public boolean isRightAlignIds(\r
+ ) {\r
+ return this._rightAlignIds;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showAnnotation'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'ShowAnnotation'.\r
*/\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
+ public boolean isShowAnnotation(\r
+ ) {\r
+ return this._showAnnotation;\r
+ }\r
\r
/**\r
- * Method hasYpos\r
+ * Returns the value of field 'showBoxes'.\r
* \r
+ * @return the value of field 'ShowBoxes'.\r
+ */\r
+ public boolean isShowBoxes(\r
+ ) {\r
+ return this._showBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showColourText'.\r
* \r
+ * @return the value of field 'ShowColourText'.\r
+ */\r
+ public boolean isShowColourText(\r
+ ) {\r
+ return this._showColourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showFullId'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'ShowFullId'.\r
*/\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \r
+ public boolean isShowFullId(\r
+ ) {\r
+ return this._showFullId;\r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Returns the value of field 'showSequenceFeatures'.\r
* \r
+ * @return the value of field 'ShowSequenceFeatures'.\r
+ */\r
+ public boolean isShowSequenceFeatures(\r
+ ) {\r
+ return this._showSequenceFeatures;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showText'.\r
* \r
+ * @return the value of field 'ShowText'.\r
+ */\r
+ public boolean isShowText(\r
+ ) {\r
+ return this._showText;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
+ * Returns the value of field 'wrapAlignment'.\r
* \r
+ * @return the value of field 'WrapAlignment'.\r
+ */\r
+ public boolean isWrapAlignment(\r
+ ) {\r
+ return this._wrapAlignment;\r
+ }\r
+\r
+ /**\r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllHiddenColumns\r
- * \r
*/\r
- public void removeAllHiddenColumns()\r
- {\r
- _hiddenColumnsList.removeAllElements();\r
- } //-- void removeAllHiddenColumns() \r
+ public void removeAllHiddenColumns(\r
+ ) {\r
+ this._hiddenColumnsList.clear();\r
+ }\r
\r
/**\r
- * Method removeHiddenColumns\r
- * \r
+ * Method removeHiddenColumns.\r
* \r
+ * @param vHiddenColumns\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {\r
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenColumnsAt.\r
* \r
* @param index\r
- * @return HiddenColumns\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
- {\r
- java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
- _hiddenColumnsList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);\r
return (jalview.schemabinding.version2.HiddenColumns) obj;\r
- } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'annotationColours'.\r
* @param annotationColours the value of field\r
* 'annotationColours'.\r
*/\r
- public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)\r
- {\r
+ public void setAnnotationColours(\r
+ final jalview.schemabinding.version2.AnnotationColours annotationColours) {\r
this._annotationColours = annotationColours;\r
- } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) \r
+ }\r
\r
/**\r
* Sets the value of field 'bgColour'.\r
* \r
* @param bgColour the value of field 'bgColour'.\r
*/\r
- public void setBgColour(java.lang.String bgColour)\r
- {\r
+ public void setBgColour(\r
+ final java.lang.String bgColour) {\r
this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
* \r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
- {\r
+ public void setConsThreshold(\r
+ final int consThreshold) {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'conservationSelected'.\r
* @param conservationSelected the value of field\r
* 'conservationSelected'.\r
*/\r
- public void setConservationSelected(boolean conservationSelected)\r
- {\r
+ public void setConservationSelected(\r
+ final boolean conservationSelected) {\r
this._conservationSelected = conservationSelected;\r
this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontName'.\r
* \r
* @param fontName the value of field 'fontName'.\r
*/\r
- public void setFontName(java.lang.String fontName)\r
- {\r
+ public void setFontName(\r
+ final java.lang.String fontName) {\r
this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontSize'.\r
* \r
* @param fontSize the value of field 'fontSize'.\r
*/\r
- public void setFontSize(int fontSize)\r
- {\r
+ public void setFontSize(\r
+ final int fontSize) {\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'fontStyle'.\r
* \r
* @param fontStyle the value of field 'fontStyle'.\r
*/\r
- public void setFontStyle(int fontStyle)\r
- {\r
+ public void setFontStyle(\r
+ final int fontStyle) {\r
this._fontStyle = fontStyle;\r
this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'gatheredViews'.\r
* \r
* @param gatheredViews the value of field 'gatheredViews'.\r
*/\r
- public void setGatheredViews(boolean gatheredViews)\r
- {\r
+ public void setGatheredViews(\r
+ final boolean gatheredViews) {\r
this._gatheredViews = gatheredViews;\r
this._has_gatheredViews = true;\r
- } //-- void setGatheredViews(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'height'.\r
* \r
* @param height the value of field 'height'.\r
*/\r
- public void setHeight(int height)\r
- {\r
+ public void setHeight(\r
+ final int height) {\r
this._height = height;\r
this._has_height = true;\r
- } //-- void setHeight(int) \r
+ }\r
\r
/**\r
- * Method setHiddenColumns\r
- * \r
* \r
* \r
* @param index\r
* @param vHiddenColumns\r
- */\r
- public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenColumns(\r
+ final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
}\r
- _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
- } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+ \r
+ this._hiddenColumnsList.set(index, vHiddenColumns);\r
+ }\r
\r
/**\r
- * Method setHiddenColumns\r
- * \r
* \r
* \r
- * @param hiddenColumnsArray\r
+ * @param vHiddenColumnsArray\r
*/\r
- public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
- {\r
+ public void setHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {\r
//-- copy array\r
- _hiddenColumnsList.removeAllElements();\r
- for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
- _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+ _hiddenColumnsList.clear();\r
+ \r
+ for (int i = 0; i < vHiddenColumnsArray.length; i++) {\r
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
}\r
- } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+ }\r
\r
/**\r
* Sets the value of field 'pidSelected'.\r
* \r
* @param pidSelected the value of field 'pidSelected'.\r
*/\r
- public void setPidSelected(boolean pidSelected)\r
- {\r
+ public void setPidSelected(\r
+ final boolean pidSelected) {\r
this._pidSelected = pidSelected;\r
this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
* \r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
+ public void setPidThreshold(\r
+ final int pidThreshold) {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'renderGaps'.\r
* \r
* @param renderGaps the value of field 'renderGaps'.\r
*/\r
- public void setRenderGaps(boolean renderGaps)\r
- {\r
+ public void setRenderGaps(\r
+ final boolean renderGaps) {\r
this._renderGaps = renderGaps;\r
this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'rightAlignIds'.\r
* \r
* @param rightAlignIds the value of field 'rightAlignIds'.\r
*/\r
- public void setRightAlignIds(boolean rightAlignIds)\r
- {\r
+ public void setRightAlignIds(\r
+ final boolean rightAlignIds) {\r
this._rightAlignIds = rightAlignIds;\r
this._has_rightAlignIds = true;\r
- } //-- void setRightAlignIds(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'sequenceSetId'.\r
* \r
* @param sequenceSetId the value of field 'sequenceSetId'.\r
*/\r
- public void setSequenceSetId(java.lang.String sequenceSetId)\r
- {\r
+ public void setSequenceSetId(\r
+ final java.lang.String sequenceSetId) {\r
this._sequenceSetId = sequenceSetId;\r
- } //-- void setSequenceSetId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'showAnnotation'.\r
* \r
* @param showAnnotation the value of field 'showAnnotation'.\r
*/\r
- public void setShowAnnotation(boolean showAnnotation)\r
- {\r
+ public void setShowAnnotation(\r
+ final boolean showAnnotation) {\r
this._showAnnotation = showAnnotation;\r
this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showBoxes'.\r
* \r
* @param showBoxes the value of field 'showBoxes'.\r
*/\r
- public void setShowBoxes(boolean showBoxes)\r
- {\r
+ public void setShowBoxes(\r
+ final boolean showBoxes) {\r
this._showBoxes = showBoxes;\r
this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showColourText'.\r
* \r
* @param showColourText the value of field 'showColourText'.\r
*/\r
- public void setShowColourText(boolean showColourText)\r
- {\r
+ public void setShowColourText(\r
+ final boolean showColourText) {\r
this._showColourText = showColourText;\r
this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showFullId'.\r
* \r
* @param showFullId the value of field 'showFullId'.\r
*/\r
- public void setShowFullId(boolean showFullId)\r
- {\r
+ public void setShowFullId(\r
+ final boolean showFullId) {\r
this._showFullId = showFullId;\r
this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showSequenceFeatures'.\r
* @param showSequenceFeatures the value of field\r
* 'showSequenceFeatures'.\r
*/\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
- {\r
+ public void setShowSequenceFeatures(\r
+ final boolean showSequenceFeatures) {\r
this._showSequenceFeatures = showSequenceFeatures;\r
this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'showText'.\r
* \r
* @param showText the value of field 'showText'.\r
*/\r
- public void setShowText(boolean showText)\r
- {\r
+ public void setShowText(\r
+ final boolean showText) {\r
this._showText = showText;\r
this._has_showText = true;\r
- } //-- void setShowText(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'startRes'.\r
* \r
* @param startRes the value of field 'startRes'.\r
*/\r
- public void setStartRes(int startRes)\r
- {\r
+ public void setStartRes(\r
+ final int startRes) {\r
this._startRes = startRes;\r
this._has_startRes = true;\r
- } //-- void setStartRes(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'startSeq'.\r
* \r
* @param startSeq the value of field 'startSeq'.\r
*/\r
- public void setStartSeq(int startSeq)\r
- {\r
+ public void setStartSeq(\r
+ final int startSeq) {\r
this._startSeq = startSeq;\r
this._has_startSeq = true;\r
- } //-- void setStartSeq(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol1'.\r
* \r
* @param textCol1 the value of field 'textCol1'.\r
*/\r
- public void setTextCol1(int textCol1)\r
- {\r
+ public void setTextCol1(\r
+ final int textCol1) {\r
this._textCol1 = textCol1;\r
this._has_textCol1 = true;\r
- } //-- void setTextCol1(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol2'.\r
* \r
* @param textCol2 the value of field 'textCol2'.\r
*/\r
- public void setTextCol2(int textCol2)\r
- {\r
+ public void setTextCol2(\r
+ final int textCol2) {\r
this._textCol2 = textCol2;\r
this._has_textCol2 = true;\r
- } //-- void setTextCol2(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textColThreshold'.\r
* \r
* @param textColThreshold the value of field 'textColThreshold'\r
*/\r
- public void setTextColThreshold(int textColThreshold)\r
- {\r
+ public void setTextColThreshold(\r
+ final int textColThreshold) {\r
this._textColThreshold = textColThreshold;\r
this._has_textColThreshold = true;\r
- } //-- void setTextColThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'title'.\r
* \r
* @param title the value of field 'title'.\r
*/\r
- public void setTitle(java.lang.String title)\r
- {\r
+ public void setTitle(\r
+ final java.lang.String title) {\r
this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'viewName'.\r
* \r
* @param viewName the value of field 'viewName'.\r
*/\r
- public void setViewName(java.lang.String viewName)\r
- {\r
+ public void setViewName(\r
+ final java.lang.String viewName) {\r
this._viewName = viewName;\r
- } //-- void setViewName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'width'.\r
* \r
* @param width the value of field 'width'.\r
*/\r
- public void setWidth(int width)\r
- {\r
+ public void setWidth(\r
+ final int width) {\r
this._width = width;\r
this._has_width = true;\r
- } //-- void setWidth(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'wrapAlignment'.\r
* \r
* @param wrapAlignment the value of field 'wrapAlignment'.\r
*/\r
- public void setWrapAlignment(boolean wrapAlignment)\r
- {\r
+ public void setWrapAlignment(\r
+ final boolean wrapAlignment) {\r
this._wrapAlignment = wrapAlignment;\r
this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'xpos'.\r
* \r
* @param xpos the value of field 'xpos'.\r
*/\r
- public void setXpos(int xpos)\r
- {\r
+ public void setXpos(\r
+ final int xpos) {\r
this._xpos = xpos;\r
this._has_xpos = true;\r
- } //-- void setXpos(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'ypos'.\r
* \r
* @param ypos the value of field 'ypos'.\r
*/\r
- public void setYpos(int ypos)\r
- {\r
+ public void setYpos(\r
+ final int ypos) {\r
this._ypos = ypos;\r
this._has_ypos = true;\r
- } //-- void setYpos(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Viewport\r
+ */\r
+ public static jalview.schemabinding.version2.Viewport unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.AnnotationColours;\r
+\r
+/**\r
+ * Class AnnotationColoursDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "AnnotationColours";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _aboveThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasAboveThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getAboveThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAboveThreshold();\r
+ return;\r
+ }\r
+ target.setAboveThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _aboveThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _annotation\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ return target.getAnnotation();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ target.setAnnotation( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotation\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _minColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasMinColour()) { return null; }\r
+ return new java.lang.Integer(target.getMinColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMinColour();\r
+ return;\r
+ }\r
+ target.setMinColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _minColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _maxColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasMaxColour()) { return null; }\r
+ return new java.lang.Integer(target.getMaxColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMaxColour();\r
+ return;\r
+ }\r
+ target.setMaxColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _maxColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourScheme\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ return target.getColourScheme();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ target.setColourScheme( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourScheme\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AnnotationColours.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Annotation;\r
+\r
+/**\r
+ * Class AnnotationDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Annotation";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _graph\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraph()) { return null; }\r
+ return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setGraph( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graph\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphType\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphType()) { return null; }\r
+ return new java.lang.Integer(target.getGraphType());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphType();\r
+ return;\r
+ }\r
+ target.setGraphType( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphType\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceRef\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getSequenceRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setSequenceRef( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceRef\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphColour()) { return null; }\r
+ return new java.lang.Integer(target.getGraphColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphColour();\r
+ return;\r
+ }\r
+ target.setGraphColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphGroup\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphGroup()) { return null; }\r
+ return new java.lang.Integer(target.getGraphGroup());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphGroup();\r
+ return;\r
+ }\r
+ target.setGraphGroup( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphGroup\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _scoreOnly\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasScoreOnly()) { return null; }\r
+ return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScoreOnly();\r
+ return;\r
+ }\r
+ target.setScoreOnly( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _scoreOnly\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _score\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasScore()) { return null; }\r
+ return new java.lang.Double(target.getScore());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScore();\r
+ return;\r
+ }\r
+ target.setScore( ((java.lang.Double) value).doubleValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _score\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.DoubleValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-1.7976931348623157E308);\r
+ typeValidator.setMaxInclusive(1.7976931348623157E308);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _visible\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasVisible()) { return null; }\r
+ return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteVisible();\r
+ return;\r
+ }\r
+ target.setVisible( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _visible\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _annotationElementList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getAnnotationElement();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.removeAllAnnotationElement();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AnnotationElement();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationElementList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _label\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getLabel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setLabel( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _label\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _thresholdLine\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getThresholdLine();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.ThresholdLine();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _thresholdLine\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Annotation.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.AnnotationElement;\r
+\r
+/**\r
+ * Class AnnotationElementDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationElementDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "annotationElement";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _position\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasPosition()) { return null; }\r
+ return new java.lang.Integer(target.getPosition());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setPosition( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _position\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _displayCharacter\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getDisplayCharacter();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setDisplayCharacter( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayCharacter\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _secondaryStructure\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getSecondaryStructure();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setSecondaryStructure( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _secondaryStructure\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ typeValidator.setLength(1);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasValue()) { return null; }\r
+ return new java.lang.Float(target.getValue());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteValue();\r
+ return;\r
+ }\r
+ target.setValue( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AnnotationElement.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Colour;\r
+\r
+/**\r
+ * Class ColourDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ColourDescriptor() {\r
+ super();\r
+ _xmlName = "colour";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _RGB\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getRGB();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setRGB( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _RGB\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Colour.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.DBRef;\r
+\r
+/**\r
+ * Class DBRefDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public DBRefDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "DBRef";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _source\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getSource();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setSource( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _source\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _accessionId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getAccessionId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setAccessionId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _accessionId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.DBRef.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Feature;\r
+\r
+/**\r
+ * Class FeatureDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "feature";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _begin\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasBegin()) { return null; }\r
+ return new java.lang.Integer(target.getBegin());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setBegin( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _begin\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _status\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getStatus();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setStatus( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _status\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _featureGroup\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getFeatureGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setFeatureGroup( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featureGroup\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _score\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasScore()) { return null; }\r
+ return new java.lang.Float(target.getScore());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScore();\r
+ return;\r
+ }\r
+ target.setScore( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _score\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _otherDataList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getOtherData();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.addOtherData( (jalview.schemabinding.version2.OtherData) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.removeAllOtherData();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.OtherData();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _otherDataList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Feature.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.FeatureSettings;\r
+\r
+/**\r
+ * Class FeatureSettingsDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureSettingsDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "FeatureSettings";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _settingList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ return target.getSetting();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.addSetting( (jalview.schemabinding.version2.Setting) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.removeAllSetting();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Setting();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _settingList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _groupList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ return target.getGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.addGroup( (jalview.schemabinding.version2.Group) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.removeAllGroup();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Group();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _groupList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.FeatureSettings.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Features;\r
+\r
+/**\r
+ * Class FeaturesDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeaturesDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "features";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ if (_identity == null) {\r
+ return super.getIdentity();\r
+ }\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Features.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Group;\r
+\r
+/**\r
+ * Class GroupDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public GroupDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "group";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Group target = (Group) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Group target = (Group) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _display\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Group target = (Group) object;\r
+ if (!target.hasDisplay()) { return null; }\r
+ return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Group target = (Group) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setDisplay( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _display\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Group.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.HiddenColumns;\r
+\r
+/**\r
+ * Class HiddenColumnsDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public HiddenColumnsDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "hiddenColumns";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStart();\r
+ return;\r
+ }\r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteEnd();\r
+ return;\r
+ }\r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.HiddenColumns.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.JGroup;\r
+\r
+/**\r
+ * Class JGroupDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JGroupDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JGroup";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStart();\r
+ return;\r
+ }\r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteEnd();\r
+ return;\r
+ }\r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.setColour( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _consThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasConsThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getConsThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConsThreshold();\r
+ return;\r
+ }\r
+ target.setConsThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _consThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasPidThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getPidThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidThreshold();\r
+ return;\r
+ }\r
+ target.setPidThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _outlineColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasOutlineColour()) { return null; }\r
+ return new java.lang.Integer(target.getOutlineColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteOutlineColour();\r
+ return;\r
+ }\r
+ target.setOutlineColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _outlineColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _displayBoxes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasDisplayBoxes()) { return null; }\r
+ return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteDisplayBoxes();\r
+ return;\r
+ }\r
+ target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayBoxes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _displayText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasDisplayText()) { return null; }\r
+ return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteDisplayText();\r
+ return;\r
+ }\r
+ target.setDisplayText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasColourText()) { return null; }\r
+ return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColourText();\r
+ return;\r
+ }\r
+ target.setColourText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextCol1()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol1();\r
+ return;\r
+ }\r
+ target.setTextCol1( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextCol2()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol2();\r
+ return;\r
+ }\r
+ target.setTextCol2( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textColThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextColThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getTextColThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextColThreshold();\r
+ return;\r
+ }\r
+ target.setTextColThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textColThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _seqList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getSeq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.addSeq( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.removeAllSeq();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _seqList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JGroup.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.JSeq;\r
+\r
+/**\r
+ * Class JSeqDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JSeqDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JSeq";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasId()) { return null; }\r
+ return new java.lang.Integer(target.getId());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setId( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hidden\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasHidden()) { return null; }\r
+ return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHidden();\r
+ return;\r
+ }\r
+ target.setHidden( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hidden\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _featuresList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getFeatures();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.addFeatures( (jalview.schemabinding.version2.Features) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllFeatures();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Features();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featuresList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pdbidsList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getPdbids();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllPdbids();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Pdbids();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pdbidsList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hiddenSequencesList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getHiddenSequences();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.addHiddenSequences( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllHiddenSequences();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenSequencesList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JSeq.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.JalviewModel;\r
+\r
+/**\r
+ * Class JalviewModelDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JalviewModel";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _creationDate\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getCreationDate();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setCreationDate( (java.util.Date) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new java.util.Date();\r
+ }\r
+ };\r
+ handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);\r
+ desc.setImmutable(true);\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _creationDate\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.DateTimeValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _vamsasModel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getVamsasModel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.VamsasModel();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _vamsasModel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _jalviewModelSequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getJalviewModelSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JalviewModelSequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _jalviewModelSequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewModel.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.JalviewModelSequence;\r
+\r
+/**\r
+ * Class JalviewModelSequenceDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelSequenceDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _JSeqList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getJSeq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addJSeq( (jalview.schemabinding.version2.JSeq) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllJSeq();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JSeq();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _JSeqList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _JGroupList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getJGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addJGroup( (jalview.schemabinding.version2.JGroup) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllJGroup();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JGroup();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _JGroupList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _viewportList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getViewport();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addViewport( (jalview.schemabinding.version2.Viewport) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllViewport();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Viewport();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _viewportList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _userColoursList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getUserColours();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addUserColours( (jalview.schemabinding.version2.UserColours) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllUserColours();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.UserColours();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _userColoursList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _treeList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getTree();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addTree( (jalview.schemabinding.version2.Tree) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllTree();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Tree();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _treeList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _featureSettings\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getFeatureSettings();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.FeatureSettings();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featureSettings\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewModelSequence.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.JalviewUserColours;\r
+import jalview.schemabinding.version2.Colour; // Added Manually\r
+/**\r
+ * Class JalviewUserColoursDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewUserColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org/colours";\r
+ _xmlName = "JalviewUserColours";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _schemeName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ return target.getSchemeName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.setSchemeName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _schemeName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _colourList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ return target.getColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.addColour( (Colour) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.removeAllColour();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new Colour();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewUserColours.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.OtherData;\r
+\r
+/**\r
+ * Class OtherDataDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public OtherDataDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "otherData";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _key\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ OtherData target = (OtherData) object;\r
+ return target.getKey();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ OtherData target = (OtherData) object;\r
+ target.setKey( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _key\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ OtherData target = (OtherData) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ OtherData target = (OtherData) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.OtherData.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Pdbentry;\r
+\r
+/**\r
+ * Class PdbentryDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryDescriptor() {\r
+ super();\r
+ _xmlName = "pdbentry";\r
+ _elementDefinition = false;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _file\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getFile();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setFile( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _file\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _items\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getPdbentryItem();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.removeAllPdbentryItem();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.PdbentryItem();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _items\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Pdbentry.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.PdbentryItem;\r
+\r
+/**\r
+ * Class PdbentryItemDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryItemDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "pdbentry";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _propertyList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ return target.getProperty();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ target.addProperty( (jalview.schemabinding.version2.Property) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ target.removeAllProperty();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Property();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _propertyList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.PdbentryItem.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Pdbids;\r
+\r
+/**\r
+ * Class PdbidsDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbidsDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "pdbids";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _structureStateList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbids target = (Pdbids) object;\r
+ return target.getStructureState();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbids target = (Pdbids) object;\r
+ target.addStructureState( (jalview.schemabinding.version2.StructureState) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Pdbids target = (Pdbids) object;\r
+ target.removeAllStructureState();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.StructureState();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _structureStateList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ if (_identity == null) {\r
+ return super.getIdentity();\r
+ }\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Pdbids.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Property;\r
+\r
+/**\r
+ * Class PropertyDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PropertyDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "property";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Property target = (Property) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Property target = (Property) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Property target = (Property) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Property target = (Property) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Property.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Sequence;\r
+\r
+/**\r
+ * Class SequenceDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Sequence";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _DBRefList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Sequence target = (Sequence) object;\r
+ return target.getDBRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.removeAllDBRef();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.DBRef();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _DBRefList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ if (_identity == null) {\r
+ return super.getIdentity();\r
+ }\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Sequence.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.SequenceSet;\r
+\r
+/**\r
+ * Class SequenceSetDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSetDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "SequenceSet";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _gapChar\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getGapChar();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.setGapChar( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _gapChar\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequenceList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllSequence();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Sequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _annotationList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getAnnotation();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllAnnotation();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Annotation();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetPropertiesList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getSequenceSetProperties();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllSequenceSetProperties();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.SequenceSetProperties();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetPropertiesList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceSet.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.SequenceSetProperties;\r
+\r
+/**\r
+ * Class SequenceSetPropertiesDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSetPropertiesDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "sequenceSetProperties";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _key\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ return target.getKey();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ target.setKey( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _key\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceSetProperties.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.SequenceType;\r
+\r
+/**\r
+ * Class SequenceTypeDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceTypeDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "SequenceType";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setSequence( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceType.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Setting;\r
+\r
+/**\r
+ * Class SettingDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SettingDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "setting";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _display\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasDisplay()) { return null; }\r
+ return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setDisplay( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _display\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _order\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasOrder()) { return null; }\r
+ return new java.lang.Float(target.getOrder());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteOrder();\r
+ return;\r
+ }\r
+ target.setOrder( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _order\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Setting.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.StructureState;\r
+\r
+/**\r
+ * Class StructureStateDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public StructureStateDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "structureState";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- _content\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ return target.getContent();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ target.setContent( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _content\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _visible\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasVisible()) { return null; }\r
+ return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteVisible();\r
+ return;\r
+ }\r
+ target.setVisible( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _visible\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.StructureState.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.ThresholdLine;\r
+\r
+/**\r
+ * Class ThresholdLineDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ThresholdLineDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "thresholdLine";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _label\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ return target.getLabel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ target.setLabel( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _label\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ if (!target.hasValue()) { return null; }\r
+ return new java.lang.Float(target.getValue());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteValue();\r
+ return;\r
+ }\r
+ target.setValue( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.ThresholdLine.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Tree;\r
+\r
+/**\r
+ * Class TreeDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public TreeDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "tree";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getFontName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setFontName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontSize\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFontSize()) { return null; }\r
+ return new java.lang.Integer(target.getFontSize());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontSize();\r
+ return;\r
+ }\r
+ target.setFontSize( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontSize\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontStyle\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFontStyle()) { return null; }\r
+ return new java.lang.Integer(target.getFontStyle());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontStyle();\r
+ return;\r
+ }\r
+ target.setFontStyle( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontStyle\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showBootstrap\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasShowBootstrap()) { return null; }\r
+ return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowBootstrap();\r
+ return;\r
+ }\r
+ target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showBootstrap\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showDistances\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasShowDistances()) { return null; }\r
+ return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowDistances();\r
+ return;\r
+ }\r
+ target.setShowDistances( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showDistances\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _markUnlinked\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasMarkUnlinked()) { return null; }\r
+ return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMarkUnlinked();\r
+ return;\r
+ }\r
+ target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _markUnlinked\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fitToWindow\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFitToWindow()) { return null; }\r
+ return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFitToWindow();\r
+ return;\r
+ }\r
+ target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fitToWindow\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _currentTree\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasCurrentTree()) { return null; }\r
+ return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteCurrentTree();\r
+ return;\r
+ }\r
+ target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _currentTree\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _title\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getTitle();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setTitle( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _title\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _newick\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getNewick();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setNewick( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _newick\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Tree.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.UserColourScheme;\r
+\r
+/**\r
+ * Class UserColourSchemeDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColourSchemeDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "UserColourScheme";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ if (_identity == null) {\r
+ return super.getIdentity();\r
+ }\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.UserColourScheme.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.UserColours;\r
+\r
+/**\r
+ * Class UserColoursDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "UserColours";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ UserColours target = (UserColours) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ UserColours target = (UserColours) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _userColourScheme\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ UserColours target = (UserColours) object;\r
+ return target.getUserColourScheme();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ UserColours target = (UserColours) object;\r
+ target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.UserColourScheme();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _userColourScheme\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.UserColours.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.VAMSAS;\r
+\r
+/**\r
+ * Class VAMSASDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VAMSASDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "VAMSAS";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _treeList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ VAMSAS target = (VAMSAS) object;\r
+ return target.getTree();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.addTree( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.removeAllTree();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _treeList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ VAMSAS target = (VAMSAS) object;\r
+ return target.getSequenceSet();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.removeAllSequenceSet();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.SequenceSet();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.VAMSAS.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.VamsasModel;\r
+\r
+/**\r
+ * Class VamsasModelDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VamsasModelDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "vamsasModel";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ if (_identity == null) {\r
+ return super.getIdentity();\r
+ }\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.VamsasModel.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Viewport;\r
+\r
+/**\r
+ * Class ViewportDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+ /**\r
+ * Field _identity.\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ViewportDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "Viewport";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _conservationSelected\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasConservationSelected()) { return null; }\r
+ return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConservationSelected();\r
+ return;\r
+ }\r
+ target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _conservationSelected\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidSelected\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasPidSelected()) { return null; }\r
+ return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidSelected();\r
+ return;\r
+ }\r
+ target.setPidSelected( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidSelected\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _bgColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getBgColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setBgColour( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _bgColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _consThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasConsThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getConsThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConsThreshold();\r
+ return;\r
+ }\r
+ target.setConsThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _consThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasPidThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getPidThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidThreshold();\r
+ return;\r
+ }\r
+ target.setPidThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _title\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getTitle();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setTitle( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _title\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showFullId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowFullId()) { return null; }\r
+ return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowFullId();\r
+ return;\r
+ }\r
+ target.setShowFullId( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showFullId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _rightAlignIds\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasRightAlignIds()) { return null; }\r
+ return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteRightAlignIds();\r
+ return;\r
+ }\r
+ target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _rightAlignIds\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowText()) { return null; }\r
+ return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowText();\r
+ return;\r
+ }\r
+ target.setShowText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showColourText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowColourText()) { return null; }\r
+ return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowColourText();\r
+ return;\r
+ }\r
+ target.setShowColourText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showColourText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showBoxes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowBoxes()) { return null; }\r
+ return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowBoxes();\r
+ return;\r
+ }\r
+ target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showBoxes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _wrapAlignment\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasWrapAlignment()) { return null; }\r
+ return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWrapAlignment();\r
+ return;\r
+ }\r
+ target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _wrapAlignment\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _renderGaps\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasRenderGaps()) { return null; }\r
+ return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteRenderGaps();\r
+ return;\r
+ }\r
+ target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _renderGaps\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showSequenceFeatures\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowSequenceFeatures()) { return null; }\r
+ return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowSequenceFeatures();\r
+ return;\r
+ }\r
+ target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showSequenceFeatures\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showAnnotation\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowAnnotation()) { return null; }\r
+ return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowAnnotation();\r
+ return;\r
+ }\r
+ target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showAnnotation\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _startRes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasStartRes()) { return null; }\r
+ return new java.lang.Integer(target.getStartRes());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStartRes();\r
+ return;\r
+ }\r
+ target.setStartRes( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _startRes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _startSeq\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasStartSeq()) { return null; }\r
+ return new java.lang.Integer(target.getStartSeq());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStartSeq();\r
+ return;\r
+ }\r
+ target.setStartSeq( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _startSeq\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getFontName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setFontName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontSize\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFontSize()) { return null; }\r
+ return new java.lang.Integer(target.getFontSize());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontSize();\r
+ return;\r
+ }\r
+ target.setFontSize( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontSize\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontStyle\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFontStyle()) { return null; }\r
+ return new java.lang.Integer(target.getFontStyle());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontStyle();\r
+ return;\r
+ }\r
+ target.setFontStyle( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontStyle\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _viewName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getViewName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setViewName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _viewName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getSequenceSetId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setSequenceSetId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _gatheredViews\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasGatheredViews()) { return null; }\r
+ return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGatheredViews();\r
+ return;\r
+ }\r
+ target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _gatheredViews\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextCol1()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol1();\r
+ return;\r
+ }\r
+ target.setTextCol1( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextCol2()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol2();\r
+ return;\r
+ }\r
+ target.setTextCol2( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textColThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextColThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getTextColThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextColThreshold();\r
+ return;\r
+ }\r
+ target.setTextColThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textColThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _annotationColours\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getAnnotationColours();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AnnotationColours();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationColours\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hiddenColumnsList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getHiddenColumns();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.removeAllHiddenColumns();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.HiddenColumns();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenColumnsList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return _identity;\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Viewport.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / commitdiff