From 13ae48dd55af238e2c25e957c5feb5a858d7e90e Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 21 Apr 2011 13:14:43 +0000 Subject: [PATCH] added graphHeight attribute to schema (JAL-784) --- schemas/vamsas.xsd | 2 + src/jalview/schemabinding/version2/.castor.cdr | 90 +- src/jalview/schemabinding/version2/AlcodMap.java | 368 +- src/jalview/schemabinding/version2/Alcodon.java | 526 +-- .../schemabinding/version2/AlcodonFrame.java | 864 ++-- src/jalview/schemabinding/version2/Annotation.java | 2117 ++++----- .../schemabinding/version2/AnnotationColours.java | 724 +-- .../schemabinding/version2/AnnotationElement.java | 680 +-- src/jalview/schemabinding/version2/Colour.java | 966 ++-- src/jalview/schemabinding/version2/DBRef.java | 438 +- src/jalview/schemabinding/version2/Feature.java | 1038 ++--- .../schemabinding/version2/FeatureSettings.java | 864 ++-- src/jalview/schemabinding/version2/Features.java | 232 +- src/jalview/schemabinding/version2/Group.java | 404 +- .../schemabinding/version2/HiddenColumns.java | 432 +- src/jalview/schemabinding/version2/JGroup.java | 2300 ++++----- src/jalview/schemabinding/version2/JSeq.java | 1628 +++---- .../schemabinding/version2/JalviewModel.java | 442 +- .../version2/JalviewModelSequence.java | 1850 ++++---- .../schemabinding/version2/JalviewUserColours.java | 662 +-- .../schemabinding/version2/MapListFrom.java | 432 +- src/jalview/schemabinding/version2/MapListTo.java | 432 +- .../schemabinding/version2/MapListType.java | 1164 ++--- src/jalview/schemabinding/version2/Mapping.java | 330 +- .../schemabinding/version2/MappingChoice.java | 340 +- src/jalview/schemabinding/version2/OtherData.java | 340 +- src/jalview/schemabinding/version2/Pdbentry.java | 704 +-- .../schemabinding/version2/PdbentryItem.java | 384 +- src/jalview/schemabinding/version2/Pdbids.java | 560 +-- src/jalview/schemabinding/version2/Property.java | 340 +- src/jalview/schemabinding/version2/Sequence.java | 622 +-- .../schemabinding/version2/SequenceSet.java | 1614 +++---- .../schemabinding/version2/SequenceType.java | 440 +- src/jalview/schemabinding/version2/Setting.java | 1332 +++--- .../schemabinding/version2/ThresholdLine.java | 482 +- src/jalview/schemabinding/version2/Tree.java | 1704 +++---- .../schemabinding/version2/UserColourScheme.java | 234 +- .../schemabinding/version2/UserColours.java | 340 +- src/jalview/schemabinding/version2/VAMSAS.java | 858 ++-- .../schemabinding/version2/VamsasModel.java | 232 +- src/jalview/schemabinding/version2/Viewport.java | 4868 ++++++++++---------- .../version2/descriptors/AlcodMapDescriptor.java | 468 +- .../version2/descriptors/AlcodonDescriptor.java | 560 +-- .../descriptors/AlcodonFrameDescriptor.java | 488 +- .../descriptors/AnnotationColoursDescriptor.java | 806 ++-- .../version2/descriptors/AnnotationDescriptor.java | 1809 ++++---- .../descriptors/AnnotationElementDescriptor.java | 810 ++-- .../version2/descriptors/ColourDescriptor.java | 1034 ++--- .../version2/descriptors/DBRefDescriptor.java | 608 +-- .../version2/descriptors/FeatureDescriptor.java | 962 ++-- .../descriptors/FeatureSettingsDescriptor.java | 488 +- .../version2/descriptors/FeaturesDescriptor.java | 302 +- .../version2/descriptors/GroupDescriptor.java | 474 +- .../descriptors/HiddenColumnsDescriptor.java | 486 +- .../version2/descriptors/JGroupDescriptor.java | 1900 ++++---- .../version2/descriptors/JSeqDescriptor.java | 1006 ++-- .../descriptors/JalviewModelDescriptor.java | 624 +-- .../JalviewModelSequenceDescriptor.java | 808 ++-- .../descriptors/JalviewUserColoursDescriptor.java | 552 +-- .../descriptors/MapListFromDescriptor.java | 486 +- .../version2/descriptors/MapListToDescriptor.java | 486 +- .../descriptors/MapListTypeDescriptor.java | 656 +-- .../descriptors/MappingChoiceDescriptor.java | 460 +- .../version2/descriptors/MappingDescriptor.java | 392 +- .../version2/descriptors/OtherDataDescriptor.java | 470 +- .../version2/descriptors/PdbentryDescriptor.java | 624 +-- .../descriptors/PdbentryItemDescriptor.java | 404 +- .../version2/descriptors/PdbidsDescriptor.java | 406 +- .../version2/descriptors/PropertyDescriptor.java | 470 +- .../version2/descriptors/SequenceDescriptor.java | 480 +- .../descriptors/SequenceSetDescriptor.java | 808 ++-- .../SequenceSetPropertiesDescriptor.java | 462 +- .../descriptors/SequenceTypeDescriptor.java | 620 +-- .../version2/descriptors/SettingDescriptor.java | 1240 ++--- .../descriptors/StructureStateDescriptor.java | 1050 ++--- .../descriptors/ThresholdLineDescriptor.java | 560 +-- .../version2/descriptors/TreeDescriptor.java | 1630 +++---- .../descriptors/UserColourSchemeDescriptor.java | 302 +- .../descriptors/UserColoursDescriptor.java | 464 +- .../version2/descriptors/VAMSASDescriptor.java | 498 +- .../descriptors/VamsasModelDescriptor.java | 302 +- .../version2/descriptors/ViewportDescriptor.java | 3916 ++++++++-------- 82 files changed, 32924 insertions(+), 32826 deletions(-) diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index ae0feca..3dd7d0d 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -195,6 +195,8 @@ use="optional" /> + + height in pixels for the graph if this is a graph-type annotation. diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index d1be982..4577127 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,45 +1,45 @@ -#Thu Feb 17 18:45:28 GMT 2011 -jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor -jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor -jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor -jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor -jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor -jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor -jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor -jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor -jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor -jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor -jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor -jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor -jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor -jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor -jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor -jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor -jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor -jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor -jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor -jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor -jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor -jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor -jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor -jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor -jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor -jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor -jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor -jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor -jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor -jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor -jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor -jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor -jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor -jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor -jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor -jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor -jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor -jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor -jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor -jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor -jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor -jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor -jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor -jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor +#Tue Apr 19 14:59:20 BST 2011 +jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor +jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor +jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor +jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor +jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor +jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor +jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor +jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor +jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor +jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor +jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor +jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor +jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor +jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor +jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor +jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor +jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor +jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor +jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor +jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor +jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor +jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor +jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor +jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor +jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor +jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor +jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor +jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor +jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor +jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor +jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor +jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor +jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor +jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor +jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor +jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor +jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor +jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor +jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor +jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor +jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor +jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor +jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor +jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java index f43acd6..61866aa 100644 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ b/src/jalview/schemabinding/version2/AlcodMap.java @@ -1,184 +1,184 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 AlcodMap. - * - * @version $Revision$ $Date$ - */ -public class AlcodMap implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal jalview id for the dnasq for this mapping. - * - */ - private java.lang.String _dnasq; - - /** - * a Mapping entry and an associated protein sequence - * - */ - private jalview.schemabinding.version2.Mapping _mapping; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodMap() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'dnasq'. The field 'dnasq' has - * the following description: internal jalview id for the dnasq - * for this mapping. - * - * - * @return the value of field 'Dnasq'. - */ - public java.lang.String getDnasq( - ) { - return this._dnasq; - } - - /** - * Returns the value of field 'mapping'. The field 'mapping' - * has the following description: a Mapping entry and an - * associated protein sequence - * - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping( - ) { - return this._mapping; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'dnasq'. The field 'dnasq' has the - * following description: internal jalview id for the dnasq for - * this mapping. - * - * - * @param dnasq the value of field 'dnasq'. - */ - public void setDnasq( - final java.lang.String dnasq) { - this._dnasq = dnasq; - } - - /** - * Sets the value of field 'mapping'. The field 'mapping' has - * the following description: a Mapping entry and an associated - * protein sequence - * - * - * @param mapping the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) { - this._mapping = mapping; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AlcodMap - */ - public static jalview.schemabinding.version2.AlcodMap unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 AlcodMap. + * + * @version $Revision$ $Date$ + */ +public class AlcodMap implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * internal jalview id for the dnasq for this mapping. + * + */ + private java.lang.String _dnasq; + + /** + * a Mapping entry and an associated protein sequence + * + */ + private jalview.schemabinding.version2.Mapping _mapping; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodMap() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'dnasq'. The field 'dnasq' has + * the following description: internal jalview id for the dnasq + * for this mapping. + * + * + * @return the value of field 'Dnasq'. + */ + public java.lang.String getDnasq( + ) { + return this._dnasq; + } + + /** + * Returns the value of field 'mapping'. The field 'mapping' + * has the following description: a Mapping entry and an + * associated protein sequence + * + * + * @return the value of field 'Mapping'. + */ + public jalview.schemabinding.version2.Mapping getMapping( + ) { + return this._mapping; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'dnasq'. The field 'dnasq' has the + * following description: internal jalview id for the dnasq for + * this mapping. + * + * + * @param dnasq the value of field 'dnasq'. + */ + public void setDnasq( + final java.lang.String dnasq) { + this._dnasq = dnasq; + } + + /** + * Sets the value of field 'mapping'. The field 'mapping' has + * the following description: a Mapping entry and an associated + * protein sequence + * + * + * @param mapping the value of field 'mapping'. + */ + public void setMapping( + final jalview.schemabinding.version2.Mapping mapping) { + this._mapping = mapping; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.AlcodMap + */ + public static jalview.schemabinding.version2.AlcodMap unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java index cffbd9a..1732401 100644 --- a/src/jalview/schemabinding/version2/Alcodon.java +++ b/src/jalview/schemabinding/version2/Alcodon.java @@ -1,263 +1,263 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Alcodon. - * - * @version $Revision$ $Date$ - */ -public class Alcodon implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _pos1. - */ - private long _pos1; - - /** - * keeps track of state for field: _pos1 - */ - private boolean _has_pos1; - - /** - * Field _pos2. - */ - private long _pos2; - - /** - * keeps track of state for field: _pos2 - */ - private boolean _has_pos2; - - /** - * Field _pos3. - */ - private long _pos3; - - /** - * keeps track of state for field: _pos3 - */ - private boolean _has_pos3; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alcodon() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deletePos1( - ) { - this._has_pos1= false; - } - - /** - */ - public void deletePos2( - ) { - this._has_pos2= false; - } - - /** - */ - public void deletePos3( - ) { - this._has_pos3= false; - } - - /** - * Returns the value of field 'pos1'. - * - * @return the value of field 'Pos1'. - */ - public long getPos1( - ) { - return this._pos1; - } - - /** - * Returns the value of field 'pos2'. - * - * @return the value of field 'Pos2'. - */ - public long getPos2( - ) { - return this._pos2; - } - - /** - * Returns the value of field 'pos3'. - * - * @return the value of field 'Pos3'. - */ - public long getPos3( - ) { - return this._pos3; - } - - /** - * Method hasPos1. - * - * @return true if at least one Pos1 has been added - */ - public boolean hasPos1( - ) { - return this._has_pos1; - } - - /** - * Method hasPos2. - * - * @return true if at least one Pos2 has been added - */ - public boolean hasPos2( - ) { - return this._has_pos2; - } - - /** - * Method hasPos3. - * - * @return true if at least one Pos3 has been added - */ - public boolean hasPos3( - ) { - return this._has_pos3; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'pos1'. - * - * @param pos1 the value of field 'pos1'. - */ - public void setPos1( - final long pos1) { - this._pos1 = pos1; - this._has_pos1 = true; - } - - /** - * Sets the value of field 'pos2'. - * - * @param pos2 the value of field 'pos2'. - */ - public void setPos2( - final long pos2) { - this._pos2 = pos2; - this._has_pos2 = true; - } - - /** - * Sets the value of field 'pos3'. - * - * @param pos3 the value of field 'pos3'. - */ - public void setPos3( - final long pos3) { - this._pos3 = pos3; - this._has_pos3 = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Alcodo - */ - public static jalview.schemabinding.version2.Alcodon unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Alcodon. + * + * @version $Revision$ $Date$ + */ +public class Alcodon implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _pos1. + */ + private long _pos1; + + /** + * keeps track of state for field: _pos1 + */ + private boolean _has_pos1; + + /** + * Field _pos2. + */ + private long _pos2; + + /** + * keeps track of state for field: _pos2 + */ + private boolean _has_pos2; + + /** + * Field _pos3. + */ + private long _pos3; + + /** + * keeps track of state for field: _pos3 + */ + private boolean _has_pos3; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Alcodon() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deletePos1( + ) { + this._has_pos1= false; + } + + /** + */ + public void deletePos2( + ) { + this._has_pos2= false; + } + + /** + */ + public void deletePos3( + ) { + this._has_pos3= false; + } + + /** + * Returns the value of field 'pos1'. + * + * @return the value of field 'Pos1'. + */ + public long getPos1( + ) { + return this._pos1; + } + + /** + * Returns the value of field 'pos2'. + * + * @return the value of field 'Pos2'. + */ + public long getPos2( + ) { + return this._pos2; + } + + /** + * Returns the value of field 'pos3'. + * + * @return the value of field 'Pos3'. + */ + public long getPos3( + ) { + return this._pos3; + } + + /** + * Method hasPos1. + * + * @return true if at least one Pos1 has been added + */ + public boolean hasPos1( + ) { + return this._has_pos1; + } + + /** + * Method hasPos2. + * + * @return true if at least one Pos2 has been added + */ + public boolean hasPos2( + ) { + return this._has_pos2; + } + + /** + * Method hasPos3. + * + * @return true if at least one Pos3 has been added + */ + public boolean hasPos3( + ) { + return this._has_pos3; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'pos1'. + * + * @param pos1 the value of field 'pos1'. + */ + public void setPos1( + final long pos1) { + this._pos1 = pos1; + this._has_pos1 = true; + } + + /** + * Sets the value of field 'pos2'. + * + * @param pos2 the value of field 'pos2'. + */ + public void setPos2( + final long pos2) { + this._pos2 = pos2; + this._has_pos2 = true; + } + + /** + * Sets the value of field 'pos3'. + * + * @param pos3 the value of field 'pos3'. + */ + public void setPos3( + final long pos3) { + this._pos3 = pos3; + this._has_pos3 = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Alcodo + */ + public static jalview.schemabinding.version2.Alcodon unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index b8b2a41..76db239 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -1,432 +1,432 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 AlcodonFrame. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrame implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alcodonList. - */ - private java.util.Vector _alcodonList; - - /** - * Field _alcodMapList. - */ - private java.util.Vector _alcodMapList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodonFrame() { - super(); - this._alcodonList = new java.util.Vector(); - this._alcodMapList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - this._alcodMapList.addElement(vAlcodMap); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodMap( - final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - this._alcodMapList.add(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - this._alcodonList.addElement(vAlcodon); - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodon( - final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - this._alcodonList.add(index, vAlcodon); - } - - /** - * Method enumerateAlcodMap. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AlcodMap elements - */ - public java.util.Enumeration enumerateAlcodMap( - ) { - return this._alcodMapList.elements(); - } - - /** - * Method enumerateAlcodon. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Alcodon elements - */ - public java.util.Enumeration enumerateAlcodon( - ) { - return this._alcodonList.elements(); - } - - /** - * Method getAlcodMap. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.AlcodMap at the given index - */ - public jalview.schemabinding.version2.AlcodMap getAlcodMap( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) { - throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index); - } - - /** - * Method getAlcodMap.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AlcodMap[] getAlcodMap( - ) { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount( - ) { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Alcodon at the given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Alcodon[] getAlcodon( - ) { - jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; - return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array); - } - - /** - * Method getAlcodonCount. - * - * @return the size of this collection - */ - public int getAlcodonCount( - ) { - return this._alcodonList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Method removeAlcodMap. - * - * @param vAlcodMap - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) { - boolean removed = _alcodMapList.remove(vAlcodMap); - return removed; - } - - /** - * Method removeAlcodMapAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( - final int index) { - java.lang.Object obj = this._alcodMapList.remove(index); - return (jalview.schemabinding.version2.AlcodMap) obj; - } - - /** - * Method removeAlcodon. - * - * @param vAlcodon - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) { - boolean removed = _alcodonList.remove(vAlcodon); - return removed; - } - - /** - * Method removeAlcodonAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Alcodon removeAlcodonAt( - final int index) { - java.lang.Object obj = this._alcodonList.remove(index); - return (jalview.schemabinding.version2.Alcodon) obj; - } - - /** - */ - public void removeAllAlcodMap( - ) { - this._alcodMapList.clear(); - } - - /** - */ - public void removeAllAlcodon( - ) { - this._alcodonList.clear(); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAlcodMap( - final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) { - throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); - } - - this._alcodMapList.set(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodMapArray - */ - public void setAlcodMap( - final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) { - //-- copy array - _alcodMapList.clear(); - - for (int i = 0; i < vAlcodMapArray.length; i++) { - this._alcodMapList.add(vAlcodMapArray[i]); - } - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAlcodon( - final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) { - throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); - } - - this._alcodonList.set(index, vAlcodon); - } - - /** - * - * - * @param vAlcodonArray - */ - public void setAlcodon( - final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) { - //-- copy array - _alcodonList.clear(); - - for (int i = 0; i < vAlcodonArray.length; i++) { - this._alcodonList.add(vAlcodonArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AlcodonFrame - */ - public static jalview.schemabinding.version2.AlcodonFrame unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 AlcodonFrame. + * + * @version $Revision$ $Date$ + */ +public class AlcodonFrame implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _alcodonList. + */ + private java.util.Vector _alcodonList; + + /** + * Field _alcodMapList. + */ + private java.util.Vector _alcodMapList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodonFrame() { + super(); + this._alcodonList = new java.util.Vector(); + this._alcodMapList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + this._alcodMapList.addElement(vAlcodMap); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodMap( + final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + this._alcodMapList.add(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + this._alcodonList.addElement(vAlcodon); + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodon( + final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + this._alcodonList.add(index, vAlcodon); + } + + /** + * Method enumerateAlcodMap. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.AlcodMap elements + */ + public java.util.Enumeration enumerateAlcodMap( + ) { + return this._alcodMapList.elements(); + } + + /** + * Method enumerateAlcodon. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Alcodon elements + */ + public java.util.Enumeration enumerateAlcodon( + ) { + return this._alcodonList.elements(); + } + + /** + * Method getAlcodMap. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AlcodMap at the given index + */ + public jalview.schemabinding.version2.AlcodMap getAlcodMap( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) { + throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index); + } + + /** + * Method getAlcodMap.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.AlcodMap[] getAlcodMap( + ) { + jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; + return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array); + } + + /** + * Method getAlcodMapCount. + * + * @return the size of this collection + */ + public int getAlcodMapCount( + ) { + return this._alcodMapList.size(); + } + + /** + * Method getAlcodon. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Alcodon at the given index + */ + public jalview.schemabinding.version2.Alcodon getAlcodon( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); + } + + /** + * Method getAlcodon.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Alcodon[] getAlcodon( + ) { + jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; + return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array); + } + + /** + * Method getAlcodonCount. + * + * @return the size of this collection + */ + public int getAlcodonCount( + ) { + return this._alcodonList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method removeAlcodMap. + * + * @param vAlcodMap + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) { + boolean removed = _alcodMapList.remove(vAlcodMap); + return removed; + } + + /** + * Method removeAlcodMapAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( + final int index) { + java.lang.Object obj = this._alcodMapList.remove(index); + return (jalview.schemabinding.version2.AlcodMap) obj; + } + + /** + * Method removeAlcodon. + * + * @param vAlcodon + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) { + boolean removed = _alcodonList.remove(vAlcodon); + return removed; + } + + /** + * Method removeAlcodonAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Alcodon removeAlcodonAt( + final int index) { + java.lang.Object obj = this._alcodonList.remove(index); + return (jalview.schemabinding.version2.Alcodon) obj; + } + + /** + */ + public void removeAllAlcodMap( + ) { + this._alcodMapList.clear(); + } + + /** + */ + public void removeAllAlcodon( + ) { + this._alcodonList.clear(); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodMap( + final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) { + throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); + } + + this._alcodMapList.set(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodMapArray + */ + public void setAlcodMap( + final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) { + //-- copy array + _alcodMapList.clear(); + + for (int i = 0; i < vAlcodMapArray.length; i++) { + this._alcodMapList.add(vAlcodMapArray[i]); + } + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodon( + final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + this._alcodonList.set(index, vAlcodon); + } + + /** + * + * + * @param vAlcodonArray + */ + public void setAlcodon( + final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) { + //-- copy array + _alcodonList.clear(); + + for (int i = 0; i < vAlcodonArray.length; i++) { + this._alcodonList.add(vAlcodonArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.AlcodonFrame + */ + public static jalview.schemabinding.version2.AlcodonFrame unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 8c5c8ff..a6d60ed 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,1032 +1,1085 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Annotation. - * - * @version $Revision$ $Date$ - */ -public class Annotation implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _graph. - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _graphType. - */ - private int _graphType; - - /** - * keeps track of state for field: _graphType - */ - private boolean _has_graphType; - - /** - * Field _sequenceRef. - */ - private java.lang.String _sequenceRef; - - /** - * Field _groupRef. - */ - private java.lang.String _groupRef; - - /** - * Field _graphColour. - */ - private int _graphColour; - - /** - * keeps track of state for field: _graphColour - */ - private boolean _has_graphColour; - - /** - * Field _graphGroup. - */ - private int _graphGroup; - - /** - * keeps track of state for field: _graphGroup - */ - private boolean _has_graphGroup; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _scoreOnly. - */ - private boolean _scoreOnly = false; - - /** - * keeps track of state for field: _scoreOnly - */ - private boolean _has_scoreOnly; - - /** - * Field _score. - */ - private double _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * Field _centreColLabels. - */ - private boolean _centreColLabels; - - /** - * keeps track of state for field: _centreColLabels - */ - private boolean _has_centreColLabels; - - /** - * Field _scaleColLabels. - */ - private boolean _scaleColLabels; - - /** - * keeps track of state for field: _scaleColLabels - */ - private boolean _has_scaleColLabels; - - /** - * Field _showAllColLabels. - */ - private boolean _showAllColLabels; - - /** - * keeps track of state for field: _showAllColLabels - */ - private boolean _has_showAllColLabels; - - /** - * is an autocalculated annotation row - */ - private boolean _autoCalculated = false; - - /** - * keeps track of state for field: _autoCalculated - */ - private boolean _has_autoCalculated; - - /** - * Field _annotationElementList. - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _thresholdLine. - */ - private jalview.schemabinding.version2.ThresholdLine _thresholdLine; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Annotation() { - super(); - this._annotationElementList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { - this._annotationElementList.addElement(vAnnotationElement); - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotationElement( - final int index, - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { - this._annotationElementList.add(index, vAnnotationElement); - } - - /** - */ - public void deleteAutoCalculated( - ) { - this._has_autoCalculated= false; - } - - /** - */ - public void deleteCentreColLabels( - ) { - this._has_centreColLabels= false; - } - - /** - */ - public void deleteGraph( - ) { - this._has_graph= false; - } - - /** - */ - public void deleteGraphColour( - ) { - this._has_graphColour= false; - } - - /** - */ - public void deleteGraphGroup( - ) { - this._has_graphGroup= false; - } - - /** - */ - public void deleteGraphType( - ) { - this._has_graphType= false; - } - - /** - */ - public void deleteScaleColLabels( - ) { - this._has_scaleColLabels= false; - } - - /** - */ - public void deleteScore( - ) { - this._has_score= false; - } - - /** - */ - public void deleteScoreOnly( - ) { - this._has_scoreOnly= false; - } - - /** - */ - public void deleteShowAllColLabels( - ) { - this._has_showAllColLabels= false; - } - - /** - */ - public void deleteVisible( - ) { - this._has_visible= false; - } - - /** - * Method enumerateAnnotationElement. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AnnotationElement elements - */ - public java.util.Enumeration enumerateAnnotationElement( - ) { - return this._annotationElementList.elements(); - } - - /** - * Method getAnnotationElement. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.AnnotationElement at the - * given index - */ - public jalview.schemabinding.version2.AnnotationElement getAnnotationElement( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index); - } - - /** - * Method getAnnotationElement.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement( - ) { - jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; - return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array); - } - - /** - * Method getAnnotationElementCount. - * - * @return the size of this collection - */ - public int getAnnotationElementCount( - ) { - return this._annotationElementList.size(); - } - - /** - * Returns the value of field 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean getAutoCalculated( - ) { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean getCentreColLabels( - ) { - return this._centreColLabels; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription( - ) { - return this._description; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean getGraph( - ) { - return this._graph; - } - - /** - * Returns the value of field 'graphColour'. - * - * @return the value of field 'GraphColour'. - */ - public int getGraphColour( - ) { - return this._graphColour; - } - - /** - * Returns the value of field 'graphGroup'. - * - * @return the value of field 'GraphGroup'. - */ - public int getGraphGroup( - ) { - return this._graphGroup; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType( - ) { - return this._graphType; - } - - /** - * Returns the value of field 'groupRef'. - * - * @return the value of field 'GroupRef'. - */ - public java.lang.String getGroupRef( - ) { - return this._groupRef; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel( - ) { - return this._label; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean getScaleColLabels( - ) { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public double getScore( - ) { - return this._score; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean getScoreOnly( - ) { - return this._scoreOnly; - } - - /** - * Returns the value of field 'sequenceRef'. - * - * @return the value of field 'SequenceRef'. - */ - public java.lang.String getSequenceRef( - ) { - return this._sequenceRef; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean getShowAllColLabels( - ) { - return this._showAllColLabels; - } - - /** - * Returns the value of field 'thresholdLine'. - * - * @return the value of field 'ThresholdLine'. - */ - public jalview.schemabinding.version2.ThresholdLine getThresholdLine( - ) { - return this._thresholdLine; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible( - ) { - return this._visible; - } - - /** - * Method hasAutoCalculated. - * - * @return true if at least one AutoCalculated has been added - */ - public boolean hasAutoCalculated( - ) { - return this._has_autoCalculated; - } - - /** - * Method hasCentreColLabels. - * - * @return true if at least one CentreColLabels has been added - */ - public boolean hasCentreColLabels( - ) { - return this._has_centreColLabels; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph( - ) { - return this._has_graph; - } - - /** - * Method hasGraphColour. - * - * @return true if at least one GraphColour has been added - */ - public boolean hasGraphColour( - ) { - return this._has_graphColour; - } - - /** - * Method hasGraphGroup. - * - * @return true if at least one GraphGroup has been added - */ - public boolean hasGraphGroup( - ) { - return this._has_graphGroup; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType( - ) { - return this._has_graphType; - } - - /** - * Method hasScaleColLabels. - * - * @return true if at least one ScaleColLabels has been added - */ - public boolean hasScaleColLabels( - ) { - return this._has_scaleColLabels; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore( - ) { - return this._has_score; - } - - /** - * Method hasScoreOnly. - * - * @return true if at least one ScoreOnly has been added - */ - public boolean hasScoreOnly( - ) { - return this._has_scoreOnly; - } - - /** - * Method hasShowAllColLabels. - * - * @return true if at least one ShowAllColLabels has been added - */ - public boolean hasShowAllColLabels( - ) { - return this._has_showAllColLabels; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible( - ) { - return this._has_visible; - } - - /** - * Returns the value of field 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean isAutoCalculated( - ) { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean isCentreColLabels( - ) { - return this._centreColLabels; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph( - ) { - return this._graph; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean isScaleColLabels( - ) { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean isScoreOnly( - ) { - return this._scoreOnly; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean isShowAllColLabels( - ) { - return this._showAllColLabels; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible( - ) { - return this._visible; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotationElement( - ) { - this._annotationElementList.clear(); - } - - /** - * Method removeAnnotationElement. - * - * @param vAnnotationElement - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( - final int index) { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.schemabinding.version2.AnnotationElement) obj; - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAnnotationElement( - final int index, - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); - } - - this._annotationElementList.set(index, vAnnotationElement); - } - - /** - * - * - * @param vAnnotationElementArray - */ - public void setAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { - //-- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @param autoCalculated the value of field 'autoCalculated'. - */ - public void setAutoCalculated( - final boolean autoCalculated) { - this._autoCalculated = autoCalculated; - this._has_autoCalculated = true; - } - - /** - * Sets the value of field 'centreColLabels'. - * - * @param centreColLabels the value of field 'centreColLabels'. - */ - public void setCentreColLabels( - final boolean centreColLabels) { - this._centreColLabels = centreColLabels; - this._has_centreColLabels = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription( - final java.lang.String description) { - this._description = description; - } - - /** - * Sets the value of field 'graph'. - * - * @param graph the value of field 'graph'. - */ - public void setGraph( - final boolean graph) { - this._graph = graph; - this._has_graph = true; - } - - /** - * Sets the value of field 'graphColour'. - * - * @param graphColour the value of field 'graphColour'. - */ - public void setGraphColour( - final int graphColour) { - this._graphColour = graphColour; - this._has_graphColour = true; - } - - /** - * Sets the value of field 'graphGroup'. - * - * @param graphGroup the value of field 'graphGroup'. - */ - public void setGraphGroup( - final int graphGroup) { - this._graphGroup = graphGroup; - this._has_graphGroup = true; - } - - /** - * Sets the value of field 'graphType'. - * - * @param graphType the value of field 'graphType'. - */ - public void setGraphType( - final int graphType) { - this._graphType = graphType; - this._has_graphType = true; - } - - /** - * Sets the value of field 'groupRef'. - * - * @param groupRef the value of field 'groupRef'. - */ - public void setGroupRef( - final java.lang.String groupRef) { - this._groupRef = groupRef; - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel( - final java.lang.String label) { - this._label = label; - } - - /** - * Sets the value of field 'scaleColLabels'. - * - * @param scaleColLabels the value of field 'scaleColLabels'. - */ - public void setScaleColLabels( - final boolean scaleColLabels) { - this._scaleColLabels = scaleColLabels; - this._has_scaleColLabels = true; - } - - /** - * Sets the value of field 'score'. - * - * @param score the value of field 'score'. - */ - public void setScore( - final double score) { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'scoreOnly'. - * - * @param scoreOnly the value of field 'scoreOnly'. - */ - public void setScoreOnly( - final boolean scoreOnly) { - this._scoreOnly = scoreOnly; - this._has_scoreOnly = true; - } - - /** - * Sets the value of field 'sequenceRef'. - * - * @param sequenceRef the value of field 'sequenceRef'. - */ - public void setSequenceRef( - final java.lang.String sequenceRef) { - this._sequenceRef = sequenceRef; - } - - /** - * Sets the value of field 'showAllColLabels'. - * - * @param showAllColLabels the value of field 'showAllColLabels' - */ - public void setShowAllColLabels( - final boolean showAllColLabels) { - this._showAllColLabels = showAllColLabels; - this._has_showAllColLabels = true; - } - - /** - * Sets the value of field 'thresholdLine'. - * - * @param thresholdLine the value of field 'thresholdLine'. - */ - public void setThresholdLine( - final jalview.schemabinding.version2.ThresholdLine thresholdLine) { - this._thresholdLine = thresholdLine; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible the value of field 'visible'. - */ - public void setVisible( - final boolean visible) { - this._visible = visible; - this._has_visible = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.Annotation - */ - public static jalview.schemabinding.version2.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Annotation. + * + * @version $Revision$ $Date$ + */ +public class Annotation implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _graph. + */ + private boolean _graph; + + /** + * keeps track of state for field: _graph + */ + private boolean _has_graph; + + /** + * Field _graphType. + */ + private int _graphType; + + /** + * keeps track of state for field: _graphType + */ + private boolean _has_graphType; + + /** + * Field _sequenceRef. + */ + private java.lang.String _sequenceRef; + + /** + * Field _groupRef. + */ + private java.lang.String _groupRef; + + /** + * Field _graphColour. + */ + private int _graphColour; + + /** + * keeps track of state for field: _graphColour + */ + private boolean _has_graphColour; + + /** + * Field _graphGroup. + */ + private int _graphGroup; + + /** + * keeps track of state for field: _graphGroup + */ + private boolean _has_graphGroup; + + /** + * height in pixels for the graph if this is a graph-type + * annotation. + */ + private int _graphHeight; + + /** + * keeps track of state for field: _graphHeight + */ + private boolean _has_graphHeight; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _scoreOnly. + */ + private boolean _scoreOnly = false; + + /** + * keeps track of state for field: _scoreOnly + */ + private boolean _has_scoreOnly; + + /** + * Field _score. + */ + private double _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _visible. + */ + private boolean _visible; + + /** + * keeps track of state for field: _visible + */ + private boolean _has_visible; + + /** + * Field _centreColLabels. + */ + private boolean _centreColLabels; + + /** + * keeps track of state for field: _centreColLabels + */ + private boolean _has_centreColLabels; + + /** + * Field _scaleColLabels. + */ + private boolean _scaleColLabels; + + /** + * keeps track of state for field: _scaleColLabels + */ + private boolean _has_scaleColLabels; + + /** + * Field _showAllColLabels. + */ + private boolean _showAllColLabels; + + /** + * keeps track of state for field: _showAllColLabels + */ + private boolean _has_showAllColLabels; + + /** + * is an autocalculated annotation row + */ + private boolean _autoCalculated = false; + + /** + * keeps track of state for field: _autoCalculated + */ + private boolean _has_autoCalculated; + + /** + * Field _annotationElementList. + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _thresholdLine. + */ + private jalview.schemabinding.version2.ThresholdLine _thresholdLine; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Annotation() { + super(); + this._annotationElementList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.addElement(vAnnotationElement); + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotationElement( + final int index, + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.add(index, vAnnotationElement); + } + + /** + */ + public void deleteAutoCalculated( + ) { + this._has_autoCalculated= false; + } + + /** + */ + public void deleteCentreColLabels( + ) { + this._has_centreColLabels= false; + } + + /** + */ + public void deleteGraph( + ) { + this._has_graph= false; + } + + /** + */ + public void deleteGraphColour( + ) { + this._has_graphColour= false; + } + + /** + */ + public void deleteGraphGroup( + ) { + this._has_graphGroup= false; + } + + /** + */ + public void deleteGraphHeight( + ) { + this._has_graphHeight= false; + } + + /** + */ + public void deleteGraphType( + ) { + this._has_graphType= false; + } + + /** + */ + public void deleteScaleColLabels( + ) { + this._has_scaleColLabels= false; + } + + /** + */ + public void deleteScore( + ) { + this._has_score= false; + } + + /** + */ + public void deleteScoreOnly( + ) { + this._has_scoreOnly= false; + } + + /** + */ + public void deleteShowAllColLabels( + ) { + this._has_showAllColLabels= false; + } + + /** + */ + public void deleteVisible( + ) { + this._has_visible= false; + } + + /** + * Method enumerateAnnotationElement. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.AnnotationElement elements + */ + public java.util.Enumeration enumerateAnnotationElement( + ) { + return this._annotationElementList.elements(); + } + + /** + * Method getAnnotationElement. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AnnotationElement at the + * given index + */ + public jalview.schemabinding.version2.AnnotationElement getAnnotationElement( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) { + throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index); + } + + /** + * Method getAnnotationElement.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement( + ) { + jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; + return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array); + } + + /** + * Method getAnnotationElementCount. + * + * @return the size of this collection + */ + public int getAnnotationElementCount( + ) { + return this._annotationElementList.size(); + } + + /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean getAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean getCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean getGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'graphColour'. + * + * @return the value of field 'GraphColour'. + */ + public int getGraphColour( + ) { + return this._graphColour; + } + + /** + * Returns the value of field 'graphGroup'. + * + * @return the value of field 'GraphGroup'. + */ + public int getGraphGroup( + ) { + return this._graphGroup; + } + + /** + * Returns the value of field 'graphHeight'. The field + * 'graphHeight' has the following description: height in + * pixels for the graph if this is a graph-type annotation. + * + * @return the value of field 'GraphHeight'. + */ + public int getGraphHeight( + ) { + return this._graphHeight; + } + + /** + * Returns the value of field 'graphType'. + * + * @return the value of field 'GraphType'. + */ + public int getGraphType( + ) { + return this._graphType; + } + + /** + * Returns the value of field 'groupRef'. + * + * @return the value of field 'GroupRef'. + */ + public java.lang.String getGroupRef( + ) { + return this._groupRef; + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean getScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public double getScore( + ) { + return this._score; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean getScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'sequenceRef'. + * + * @return the value of field 'SequenceRef'. + */ + public java.lang.String getSequenceRef( + ) { + return this._sequenceRef; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean getShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * Returns the value of field 'thresholdLine'. + * + * @return the value of field 'ThresholdLine'. + */ + public jalview.schemabinding.version2.ThresholdLine getThresholdLine( + ) { + return this._thresholdLine; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean getVisible( + ) { + return this._visible; + } + + /** + * Method hasAutoCalculated. + * + * @return true if at least one AutoCalculated has been added + */ + public boolean hasAutoCalculated( + ) { + return this._has_autoCalculated; + } + + /** + * Method hasCentreColLabels. + * + * @return true if at least one CentreColLabels has been added + */ + public boolean hasCentreColLabels( + ) { + return this._has_centreColLabels; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph( + ) { + return this._has_graph; + } + + /** + * Method hasGraphColour. + * + * @return true if at least one GraphColour has been added + */ + public boolean hasGraphColour( + ) { + return this._has_graphColour; + } + + /** + * Method hasGraphGroup. + * + * @return true if at least one GraphGroup has been added + */ + public boolean hasGraphGroup( + ) { + return this._has_graphGroup; + } + + /** + * Method hasGraphHeight. + * + * @return true if at least one GraphHeight has been added + */ + public boolean hasGraphHeight( + ) { + return this._has_graphHeight; + } + + /** + * Method hasGraphType. + * + * @return true if at least one GraphType has been added + */ + public boolean hasGraphType( + ) { + return this._has_graphType; + } + + /** + * Method hasScaleColLabels. + * + * @return true if at least one ScaleColLabels has been added + */ + public boolean hasScaleColLabels( + ) { + return this._has_scaleColLabels; + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * Method hasScoreOnly. + * + * @return true if at least one ScoreOnly has been added + */ + public boolean hasScoreOnly( + ) { + return this._has_scoreOnly; + } + + /** + * Method hasShowAllColLabels. + * + * @return true if at least one ShowAllColLabels has been added + */ + public boolean hasShowAllColLabels( + ) { + return this._has_showAllColLabels; + } + + /** + * Method hasVisible. + * + * @return true if at least one Visible has been added + */ + public boolean hasVisible( + ) { + return this._has_visible; + } + + /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean isAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean isCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean isGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean isScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean isScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean isShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean isVisible( + ) { + return this._visible; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllAnnotationElement( + ) { + this._annotationElementList.clear(); + } + + /** + * Method removeAnnotationElement. + * + * @param vAnnotationElement + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( + final int index) { + java.lang.Object obj = this._annotationElementList.remove(index); + return (jalview.schemabinding.version2.AnnotationElement) obj; + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotationElement( + final int index, + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) { + throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); + } + + this._annotationElementList.set(index, vAnnotationElement); + } + + /** + * + * + * @param vAnnotationElementArray + */ + public void setAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { + //-- copy array + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) { + this._annotationElementList.add(vAnnotationElementArray[i]); + } + } + + /** + * Sets the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @param autoCalculated the value of field 'autoCalculated'. + */ + public void setAutoCalculated( + final boolean autoCalculated) { + this._autoCalculated = autoCalculated; + this._has_autoCalculated = true; + } + + /** + * Sets the value of field 'centreColLabels'. + * + * @param centreColLabels the value of field 'centreColLabels'. + */ + public void setCentreColLabels( + final boolean centreColLabels) { + this._centreColLabels = centreColLabels; + this._has_centreColLabels = true; + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'graph'. + * + * @param graph the value of field 'graph'. + */ + public void setGraph( + final boolean graph) { + this._graph = graph; + this._has_graph = true; + } + + /** + * Sets the value of field 'graphColour'. + * + * @param graphColour the value of field 'graphColour'. + */ + public void setGraphColour( + final int graphColour) { + this._graphColour = graphColour; + this._has_graphColour = true; + } + + /** + * Sets the value of field 'graphGroup'. + * + * @param graphGroup the value of field 'graphGroup'. + */ + public void setGraphGroup( + final int graphGroup) { + this._graphGroup = graphGroup; + this._has_graphGroup = true; + } + + /** + * Sets the value of field 'graphHeight'. The field + * 'graphHeight' has the following description: height in + * pixels for the graph if this is a graph-type annotation. + * + * @param graphHeight the value of field 'graphHeight'. + */ + public void setGraphHeight( + final int graphHeight) { + this._graphHeight = graphHeight; + this._has_graphHeight = true; + } + + /** + * Sets the value of field 'graphType'. + * + * @param graphType the value of field 'graphType'. + */ + public void setGraphType( + final int graphType) { + this._graphType = graphType; + this._has_graphType = true; + } + + /** + * Sets the value of field 'groupRef'. + * + * @param groupRef the value of field 'groupRef'. + */ + public void setGroupRef( + final java.lang.String groupRef) { + this._groupRef = groupRef; + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * Sets the value of field 'scaleColLabels'. + * + * @param scaleColLabels the value of field 'scaleColLabels'. + */ + public void setScaleColLabels( + final boolean scaleColLabels) { + this._scaleColLabels = scaleColLabels; + this._has_scaleColLabels = true; + } + + /** + * Sets the value of field 'score'. + * + * @param score the value of field 'score'. + */ + public void setScore( + final double score) { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'scoreOnly'. + * + * @param scoreOnly the value of field 'scoreOnly'. + */ + public void setScoreOnly( + final boolean scoreOnly) { + this._scoreOnly = scoreOnly; + this._has_scoreOnly = true; + } + + /** + * Sets the value of field 'sequenceRef'. + * + * @param sequenceRef the value of field 'sequenceRef'. + */ + public void setSequenceRef( + final java.lang.String sequenceRef) { + this._sequenceRef = sequenceRef; + } + + /** + * Sets the value of field 'showAllColLabels'. + * + * @param showAllColLabels the value of field 'showAllColLabels' + */ + public void setShowAllColLabels( + final boolean showAllColLabels) { + this._showAllColLabels = showAllColLabels; + this._has_showAllColLabels = true; + } + + /** + * Sets the value of field 'thresholdLine'. + * + * @param thresholdLine the value of field 'thresholdLine'. + */ + public void setThresholdLine( + final jalview.schemabinding.version2.ThresholdLine thresholdLine) { + this._thresholdLine = thresholdLine; + } + + /** + * Sets the value of field 'visible'. + * + * @param visible the value of field 'visible'. + */ + public void setVisible( + final boolean visible) { + this._visible = visible; + this._has_visible = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.Annotation + */ + public static jalview.schemabinding.version2.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java index 36f9f93..96ab9d8 100755 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -1,362 +1,362 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 AnnotationColours. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColours implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _aboveThreshold. - */ - private int _aboveThreshold; - - /** - * keeps track of state for field: _aboveThreshold - */ - private boolean _has_aboveThreshold; - - /** - * Field _annotation. - */ - private java.lang.String _annotation; - - /** - * Field _minColour. - */ - private int _minColour; - - /** - * keeps track of state for field: _minColour - */ - private boolean _has_minColour; - - /** - * Field _maxColour. - */ - private int _maxColour; - - /** - * keeps track of state for field: _maxColour - */ - private boolean _has_maxColour; - - /** - * Field _colourScheme. - */ - private java.lang.String _colourScheme; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationColours() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteAboveThreshold( - ) { - this._has_aboveThreshold= false; - } - - /** - */ - public void deleteMaxColour( - ) { - this._has_maxColour= false; - } - - /** - */ - public void deleteMinColour( - ) { - this._has_minColour= false; - } - - /** - */ - public void deleteThreshold( - ) { - this._has_threshold= false; - } - - /** - * Returns the value of field 'aboveThreshold'. - * - * @return the value of field 'AboveThreshold'. - */ - public int getAboveThreshold( - ) { - return this._aboveThreshold; - } - - /** - * Returns the value of field 'annotation'. - * - * @return the value of field 'Annotation'. - */ - public java.lang.String getAnnotation( - ) { - return this._annotation; - } - - /** - * Returns the value of field 'colourScheme'. - * - * @return the value of field 'ColourScheme'. - */ - public java.lang.String getColourScheme( - ) { - return this._colourScheme; - } - - /** - * Returns the value of field 'maxColour'. - * - * @return the value of field 'MaxColour'. - */ - public int getMaxColour( - ) { - return this._maxColour; - } - - /** - * Returns the value of field 'minColour'. - * - * @return the value of field 'MinColour'. - */ - public int getMinColour( - ) { - return this._minColour; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold( - ) { - return this._threshold; - } - - /** - * Method hasAboveThreshold. - * - * @return true if at least one AboveThreshold has been added - */ - public boolean hasAboveThreshold( - ) { - return this._has_aboveThreshold; - } - - /** - * Method hasMaxColour. - * - * @return true if at least one MaxColour has been added - */ - public boolean hasMaxColour( - ) { - return this._has_maxColour; - } - - /** - * Method hasMinColour. - * - * @return true if at least one MinColour has been added - */ - public boolean hasMinColour( - ) { - return this._has_minColour; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold( - ) { - return this._has_threshold; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'aboveThreshold'. - * - * @param aboveThreshold the value of field 'aboveThreshold'. - */ - public void setAboveThreshold( - final int aboveThreshold) { - this._aboveThreshold = aboveThreshold; - this._has_aboveThreshold = true; - } - - /** - * Sets the value of field 'annotation'. - * - * @param annotation the value of field 'annotation'. - */ - public void setAnnotation( - final java.lang.String annotation) { - this._annotation = annotation; - } - - /** - * Sets the value of field 'colourScheme'. - * - * @param colourScheme the value of field 'colourScheme'. - */ - public void setColourScheme( - final java.lang.String colourScheme) { - this._colourScheme = colourScheme; - } - - /** - * Sets the value of field 'maxColour'. - * - * @param maxColour the value of field 'maxColour'. - */ - public void setMaxColour( - final int maxColour) { - this._maxColour = maxColour; - this._has_maxColour = true; - } - - /** - * Sets the value of field 'minColour'. - * - * @param minColour the value of field 'minColour'. - */ - public void setMinColour( - final int minColour) { - this._minColour = minColour; - this._has_minColour = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold the value of field 'threshold'. - */ - public void setThreshold( - final float threshold) { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AnnotationColours - */ - public static jalview.schemabinding.version2.AnnotationColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 AnnotationColours. + * + * @version $Revision$ $Date$ + */ +public class AnnotationColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _aboveThreshold. + */ + private int _aboveThreshold; + + /** + * keeps track of state for field: _aboveThreshold + */ + private boolean _has_aboveThreshold; + + /** + * Field _annotation. + */ + private java.lang.String _annotation; + + /** + * Field _minColour. + */ + private int _minColour; + + /** + * keeps track of state for field: _minColour + */ + private boolean _has_minColour; + + /** + * Field _maxColour. + */ + private int _maxColour; + + /** + * keeps track of state for field: _maxColour + */ + private boolean _has_maxColour; + + /** + * Field _colourScheme. + */ + private java.lang.String _colourScheme; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationColours() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAboveThreshold( + ) { + this._has_aboveThreshold= false; + } + + /** + */ + public void deleteMaxColour( + ) { + this._has_maxColour= false; + } + + /** + */ + public void deleteMinColour( + ) { + this._has_minColour= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'aboveThreshold'. + * + * @return the value of field 'AboveThreshold'. + */ + public int getAboveThreshold( + ) { + return this._aboveThreshold; + } + + /** + * Returns the value of field 'annotation'. + * + * @return the value of field 'Annotation'. + */ + public java.lang.String getAnnotation( + ) { + return this._annotation; + } + + /** + * Returns the value of field 'colourScheme'. + * + * @return the value of field 'ColourScheme'. + */ + public java.lang.String getColourScheme( + ) { + return this._colourScheme; + } + + /** + * Returns the value of field 'maxColour'. + * + * @return the value of field 'MaxColour'. + */ + public int getMaxColour( + ) { + return this._maxColour; + } + + /** + * Returns the value of field 'minColour'. + * + * @return the value of field 'MinColour'. + */ + public int getMinColour( + ) { + return this._minColour; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAboveThreshold. + * + * @return true if at least one AboveThreshold has been added + */ + public boolean hasAboveThreshold( + ) { + return this._has_aboveThreshold; + } + + /** + * Method hasMaxColour. + * + * @return true if at least one MaxColour has been added + */ + public boolean hasMaxColour( + ) { + return this._has_maxColour; + } + + /** + * Method hasMinColour. + * + * @return true if at least one MinColour has been added + */ + public boolean hasMinColour( + ) { + return this._has_minColour; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'aboveThreshold'. + * + * @param aboveThreshold the value of field 'aboveThreshold'. + */ + public void setAboveThreshold( + final int aboveThreshold) { + this._aboveThreshold = aboveThreshold; + this._has_aboveThreshold = true; + } + + /** + * Sets the value of field 'annotation'. + * + * @param annotation the value of field 'annotation'. + */ + public void setAnnotation( + final java.lang.String annotation) { + this._annotation = annotation; + } + + /** + * Sets the value of field 'colourScheme'. + * + * @param colourScheme the value of field 'colourScheme'. + */ + public void setColourScheme( + final java.lang.String colourScheme) { + this._colourScheme = colourScheme; + } + + /** + * Sets the value of field 'maxColour'. + * + * @param maxColour the value of field 'maxColour'. + */ + public void setMaxColour( + final int maxColour) { + this._maxColour = maxColour; + this._has_maxColour = true; + } + + /** + * Sets the value of field 'minColour'. + * + * @param minColour the value of field 'minColour'. + */ + public void setMinColour( + final int minColour) { + this._minColour = minColour; + this._has_minColour = true; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.AnnotationColours + */ + public static jalview.schemabinding.version2.AnnotationColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java index eca3e6a..6df737f 100755 --- a/src/jalview/schemabinding/version2/AnnotationElement.java +++ b/src/jalview/schemabinding/version2/AnnotationElement.java @@ -1,340 +1,340 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _position. - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _displayCharacter. - */ - private java.lang.String _displayCharacter; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure. - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElement() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteColour( - ) { - this._has_colour= false; - } - - /** - */ - public void deletePosition( - ) { - this._has_position= false; - } - - /** - */ - public void deleteValue( - ) { - this._has_value= false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour( - ) { - return this._colour; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription( - ) { - return this._description; - } - - /** - * Returns the value of field 'displayCharacter'. - * - * @return the value of field 'DisplayCharacter'. - */ - public java.lang.String getDisplayCharacter( - ) { - return this._displayCharacter; - } - - /** - * Returns the value of field 'position'. - * - * @return the value of field 'Position'. - */ - public int getPosition( - ) { - return this._position; - } - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return the value of field 'SecondaryStructure'. - */ - public java.lang.String getSecondaryStructure( - ) { - return this._secondaryStructure; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue( - ) { - return this._value; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour( - ) { - return this._has_colour; - } - - /** - * Method hasPosition. - * - * @return true if at least one Position has been added - */ - public boolean hasPosition( - ) { - return this._has_position; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue( - ) { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour( - final int colour) { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription( - final java.lang.String description) { - this._description = description; - } - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter the value of field 'displayCharacter' - */ - public void setDisplayCharacter( - final java.lang.String displayCharacter) { - this._displayCharacter = displayCharacter; - } - - /** - * Sets the value of field 'position'. - * - * @param position the value of field 'position'. - */ - public void setPosition( - final int position) { - this._position = position; - this._has_position = true; - } - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure the value of field - * 'secondaryStructure'. - */ - public void setSecondaryStructure( - final java.lang.String secondaryStructure) { - this._secondaryStructure = secondaryStructure; - } - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue( - final float value) { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AnnotationElement - */ - public static jalview.schemabinding.version2.AnnotationElement unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 AnnotationElement. + * + * @version $Revision$ $Date$ + */ +public class AnnotationElement implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _position. + */ + private int _position; + + /** + * keeps track of state for field: _position + */ + private boolean _has_position; + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _displayCharacter. + */ + private java.lang.String _displayCharacter; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _secondaryStructure. + */ + private java.lang.String _secondaryStructure; + + /** + * Field _value. + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElement() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deletePosition( + ) { + this._has_position= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'displayCharacter'. + * + * @return the value of field 'DisplayCharacter'. + */ + public java.lang.String getDisplayCharacter( + ) { + return this._displayCharacter; + } + + /** + * Returns the value of field 'position'. + * + * @return the value of field 'Position'. + */ + public int getPosition( + ) { + return this._position; + } + + /** + * Returns the value of field 'secondaryStructure'. + * + * @return the value of field 'SecondaryStructure'. + */ + public java.lang.String getSecondaryStructure( + ) { + return this._secondaryStructure; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public float getValue( + ) { + return this._value; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasPosition. + * + * @return true if at least one Position has been added + */ + public boolean hasPosition( + ) { + return this._has_position; + } + + /** + * Method hasValue. + * + * @return true if at least one Value has been added + */ + public boolean hasValue( + ) { + return this._has_value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'displayCharacter'. + * + * @param displayCharacter the value of field 'displayCharacter' + */ + public void setDisplayCharacter( + final java.lang.String displayCharacter) { + this._displayCharacter = displayCharacter; + } + + /** + * Sets the value of field 'position'. + * + * @param position the value of field 'position'. + */ + public void setPosition( + final int position) { + this._position = position; + this._has_position = true; + } + + /** + * Sets the value of field 'secondaryStructure'. + * + * @param secondaryStructure the value of field + * 'secondaryStructure'. + */ + public void setSecondaryStructure( + final java.lang.String secondaryStructure) { + this._secondaryStructure = secondaryStructure; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final float value) { + this._value = value; + this._has_value = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.AnnotationElement + */ + public static jalview.schemabinding.version2.AnnotationElement unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java index d7650a0..d64263d 100755 --- a/src/jalview/schemabinding/version2/Colour.java +++ b/src/jalview/schemabinding/version2/Colour.java @@ -1,483 +1,483 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Colour. - * - * @version $Revision$ $Date$ - */ -public class Colour implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _RGB. - */ - private java.lang.String _RGB; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * loosely specified enumeration: NONE,ABOVE, or BELOW - */ - private java.lang.String _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Colour() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteAutoScale( - ) { - this._has_autoScale= false; - } - - /** - */ - public void deleteColourByLabel( - ) { - this._has_colourByLabel= false; - } - - /** - */ - public void deleteMax( - ) { - this._has_max= false; - } - - /** - */ - public void deleteMin( - ) { - this._has_min= false; - } - - /** - */ - public void deleteThreshold( - ) { - this._has_threshold= false; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale( - ) { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel( - ) { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax( - ) { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin( - ) { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB( - ) { - return this._minRGB; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName( - ) { - return this._name; - } - - /** - * Returns the value of field 'RGB'. - * - * @return the value of field 'RGB'. - */ - public java.lang.String getRGB( - ) { - return this._RGB; - } - - /** - * Returns the value of field 'threshType'. The field - * 'threshType' has the following description: loosely - * specified enumeration: NONE,ABOVE, or BELOW - * - * @return the value of field 'ThreshType'. - */ - public java.lang.String getThreshType( - ) { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold( - ) { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale( - ) { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel( - ) { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax( - ) { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin( - ) { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold( - ) { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale( - ) { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel( - ) { - return this._colourByLabel; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale the value of field 'autoScale'. - */ - public void setAutoScale( - final boolean autoScale) { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel the value of field 'colourByLabel'. - */ - public void setColourByLabel( - final boolean colourByLabel) { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max the value of field 'max'. - */ - public void setMax( - final float max) { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min the value of field 'min'. - */ - public void setMin( - final float min) { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB the value of field 'minRGB'. - */ - public void setMinRGB( - final java.lang.String minRGB) { - this._minRGB = minRGB; - } - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName( - final java.lang.String name) { - this._name = name; - } - - /** - * Sets the value of field 'RGB'. - * - * @param RGB the value of field 'RGB'. - */ - public void setRGB( - final java.lang.String RGB) { - this._RGB = RGB; - } - - /** - * Sets the value of field 'threshType'. The field 'threshType' - * has the following description: loosely specified - * enumeration: NONE,ABOVE, or BELOW - * - * @param threshType the value of field 'threshType'. - */ - public void setThreshType( - final java.lang.String threshType) { - this._threshType = threshType; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold the value of field 'threshold'. - */ - public void setThreshold( - final float threshold) { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Colour - */ - public static jalview.schemabinding.version2.Colour unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Colour. + * + * @version $Revision$ $Date$ + */ +public class Colour implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _RGB. + */ + private java.lang.String _RGB; + + /** + * Field _minRGB. + */ + private java.lang.String _minRGB; + + /** + * loosely specified enumeration: NONE,ABOVE, or BELOW + */ + private java.lang.String _threshType; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Colour() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** + * Returns the value of field 'minRGB'. + * + * @return the value of field 'MinRGB'. + */ + public java.lang.String getMinRGB( + ) { + return this._minRGB; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'RGB'. + * + * @return the value of field 'RGB'. + */ + public java.lang.String getRGB( + ) { + return this._RGB; + } + + /** + * Returns the value of field 'threshType'. The field + * 'threshType' has the following description: loosely + * specified enumeration: NONE,ABOVE, or BELOW + * + * @return the value of field 'ThreshType'. + */ + public java.lang.String getThreshType( + ) { + return this._threshType; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** + * Sets the value of field 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'minRGB'. + * + * @param minRGB the value of field 'minRGB'. + */ + public void setMinRGB( + final java.lang.String minRGB) { + this._minRGB = minRGB; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'RGB'. + * + * @param RGB the value of field 'RGB'. + */ + public void setRGB( + final java.lang.String RGB) { + this._RGB = RGB; + } + + /** + * Sets the value of field 'threshType'. The field 'threshType' + * has the following description: loosely specified + * enumeration: NONE,ABOVE, or BELOW + * + * @param threshType the value of field 'threshType'. + */ + public void setThreshType( + final java.lang.String threshType) { + this._threshType = threshType; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Colour + */ + public static jalview.schemabinding.version2.Colour unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java index 4d67250..3917e13 100644 --- a/src/jalview/schemabinding/version2/DBRef.java +++ b/src/jalview/schemabinding/version2/DBRef.java @@ -1,219 +1,219 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 DBRef. - * - * @version $Revision$ $Date$ - */ -public class DBRef implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _source. - */ - private java.lang.String _source; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _accessionId. - */ - private java.lang.String _accessionId; - - /** - * Field _mapping. - */ - private jalview.schemabinding.version2.Mapping _mapping; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DBRef() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'accessionId'. - * - * @return the value of field 'AccessionId'. - */ - public java.lang.String getAccessionId( - ) { - return this._accessionId; - } - - /** - * Returns the value of field 'mapping'. - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping( - ) { - return this._mapping; - } - - /** - * Returns the value of field 'source'. - * - * @return the value of field 'Source'. - */ - public java.lang.String getSource( - ) { - return this._source; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion( - ) { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'accessionId'. - * - * @param accessionId the value of field 'accessionId'. - */ - public void setAccessionId( - final java.lang.String accessionId) { - this._accessionId = accessionId; - } - - /** - * Sets the value of field 'mapping'. - * - * @param mapping the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) { - this._mapping = mapping; - } - - /** - * Sets the value of field 'source'. - * - * @param source the value of field 'source'. - */ - public void setSource( - final java.lang.String source) { - this._source = source; - } - - /** - * Sets the value of field 'version'. - * - * @param version the value of field 'version'. - */ - public void setVersion( - final java.lang.String version) { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.DBRef - */ - public static jalview.schemabinding.version2.DBRef unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 DBRef. + * + * @version $Revision$ $Date$ + */ +public class DBRef implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _source. + */ + private java.lang.String _source; + + /** + * Field _version. + */ + private java.lang.String _version; + + /** + * Field _accessionId. + */ + private java.lang.String _accessionId; + + /** + * Field _mapping. + */ + private jalview.schemabinding.version2.Mapping _mapping; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DBRef() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'accessionId'. + * + * @return the value of field 'AccessionId'. + */ + public java.lang.String getAccessionId( + ) { + return this._accessionId; + } + + /** + * Returns the value of field 'mapping'. + * + * @return the value of field 'Mapping'. + */ + public jalview.schemabinding.version2.Mapping getMapping( + ) { + return this._mapping; + } + + /** + * Returns the value of field 'source'. + * + * @return the value of field 'Source'. + */ + public java.lang.String getSource( + ) { + return this._source; + } + + /** + * Returns the value of field 'version'. + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'accessionId'. + * + * @param accessionId the value of field 'accessionId'. + */ + public void setAccessionId( + final java.lang.String accessionId) { + this._accessionId = accessionId; + } + + /** + * Sets the value of field 'mapping'. + * + * @param mapping the value of field 'mapping'. + */ + public void setMapping( + final jalview.schemabinding.version2.Mapping mapping) { + this._mapping = mapping; + } + + /** + * Sets the value of field 'source'. + * + * @param source the value of field 'source'. + */ + public void setSource( + final java.lang.String source) { + this._source = source; + } + + /** + * Sets the value of field 'version'. + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.DBRef + */ + public static jalview.schemabinding.version2.DBRef unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index 109ec6e..c1bbb25 100755 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,519 +1,519 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _begin. - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _status. - */ - private java.lang.String _status; - - /** - * Field _featureGroup. - */ - private java.lang.String _featureGroup; - - /** - * Field _score. - */ - private float _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _otherDataList. - */ - private java.util.Vector _otherDataList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Feature() { - super(); - this._otherDataList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException { - this._otherDataList.addElement(vOtherData); - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addOtherData( - final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException { - this._otherDataList.add(index, vOtherData); - } - - /** - */ - public void deleteBegin( - ) { - this._has_begin= false; - } - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteScore( - ) { - this._has_score= false; - } - - /** - * Method enumerateOtherData. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.OtherData elements - */ - public java.util.Enumeration enumerateOtherData( - ) { - return this._otherDataList.elements(); - } - - /** - * Returns the value of field 'begin'. - * - * @return the value of field 'Begin'. - */ - public int getBegin( - ) { - return this._begin; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription( - ) { - return this._description; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'featureGroup'. - * - * @return the value of field 'FeatureGroup'. - */ - public java.lang.String getFeatureGroup( - ) { - return this._featureGroup; - } - - /** - * Method getOtherData. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.OtherData at the given index - */ - public jalview.schemabinding.version2.OtherData getOtherData( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) { - throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index); - } - - /** - * Method getOtherData.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.OtherData[] getOtherData( - ) { - jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; - return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array); - } - - /** - * Method getOtherDataCount. - * - * @return the size of this collection - */ - public int getOtherDataCount( - ) { - return this._otherDataList.size(); - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public float getScore( - ) { - return this._score; - } - - /** - * Returns the value of field 'status'. - * - * @return the value of field 'Status'. - */ - public java.lang.String getStatus( - ) { - return this._status; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType( - ) { - return this._type; - } - - /** - * Method hasBegin. - * - * @return true if at least one Begin has been added - */ - public boolean hasBegin( - ) { - return this._has_begin; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore( - ) { - return this._has_score; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllOtherData( - ) { - this._otherDataList.clear(); - } - - /** - * Method removeOtherData. - * - * @param vOtherData - * @return true if the object was removed from the collection. - */ - public boolean removeOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) { - boolean removed = _otherDataList.remove(vOtherData); - return removed; - } - - /** - * Method removeOtherDataAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.OtherData removeOtherDataAt( - final int index) { - java.lang.Object obj = this._otherDataList.remove(index); - return (jalview.schemabinding.version2.OtherData) obj; - } - - /** - * Sets the value of field 'begin'. - * - * @param begin the value of field 'begin'. - */ - public void setBegin( - final int begin) { - this._begin = begin; - this._has_begin = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription( - final java.lang.String description) { - this._description = description; - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'featureGroup'. - * - * @param featureGroup the value of field 'featureGroup'. - */ - public void setFeatureGroup( - final java.lang.String featureGroup) { - this._featureGroup = featureGroup; - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setOtherData( - final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) { - throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); - } - - this._otherDataList.set(index, vOtherData); - } - - /** - * - * - * @param vOtherDataArray - */ - public void setOtherData( - final jalview.schemabinding.version2.OtherData[] vOtherDataArray) { - //-- copy array - _otherDataList.clear(); - - for (int i = 0; i < vOtherDataArray.length; i++) { - this._otherDataList.add(vOtherDataArray[i]); - } - } - - /** - * Sets the value of field 'score'. - * - * @param score the value of field 'score'. - */ - public void setScore( - final float score) { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'status'. - * - * @param status the value of field 'status'. - */ - public void setStatus( - final java.lang.String status) { - this._status = status; - } - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType( - final java.lang.String type) { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Feature. + * + * @version $Revision$ $Date$ + */ +public class Feature implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _begin. + */ + private int _begin; + + /** + * keeps track of state for field: _begin + */ + private boolean _has_begin; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _status. + */ + private java.lang.String _status; + + /** + * Field _featureGroup. + */ + private java.lang.String _featureGroup; + + /** + * Field _score. + */ + private float _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _otherDataList. + */ + private java.util.Vector _otherDataList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Feature() { + super(); + this._otherDataList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + this._otherDataList.addElement(vOtherData); + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addOtherData( + final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + this._otherDataList.add(index, vOtherData); + } + + /** + */ + public void deleteBegin( + ) { + this._has_begin= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteScore( + ) { + this._has_score= false; + } + + /** + * Method enumerateOtherData. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.OtherData elements + */ + public java.util.Enumeration enumerateOtherData( + ) { + return this._otherDataList.elements(); + } + + /** + * Returns the value of field 'begin'. + * + * @return the value of field 'Begin'. + */ + public int getBegin( + ) { + return this._begin; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'featureGroup'. + * + * @return the value of field 'FeatureGroup'. + */ + public java.lang.String getFeatureGroup( + ) { + return this._featureGroup; + } + + /** + * Method getOtherData. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.OtherData at the given index + */ + public jalview.schemabinding.version2.OtherData getOtherData( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) { + throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index); + } + + /** + * Method getOtherData.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.OtherData[] getOtherData( + ) { + jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; + return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array); + } + + /** + * Method getOtherDataCount. + * + * @return the size of this collection + */ + public int getOtherDataCount( + ) { + return this._otherDataList.size(); + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public float getScore( + ) { + return this._score; + } + + /** + * Returns the value of field 'status'. + * + * @return the value of field 'Status'. + */ + public java.lang.String getStatus( + ) { + return this._status; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method hasBegin. + * + * @return true if at least one Begin has been added + */ + public boolean hasBegin( + ) { + return this._has_begin; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllOtherData( + ) { + this._otherDataList.clear(); + } + + /** + * Method removeOtherData. + * + * @param vOtherData + * @return true if the object was removed from the collection. + */ + public boolean removeOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) { + boolean removed = _otherDataList.remove(vOtherData); + return removed; + } + + /** + * Method removeOtherDataAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.OtherData removeOtherDataAt( + final int index) { + java.lang.Object obj = this._otherDataList.remove(index); + return (jalview.schemabinding.version2.OtherData) obj; + } + + /** + * Sets the value of field 'begin'. + * + * @param begin the value of field 'begin'. + */ + public void setBegin( + final int begin) { + this._begin = begin; + this._has_begin = true; + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'featureGroup'. + * + * @param featureGroup the value of field 'featureGroup'. + */ + public void setFeatureGroup( + final java.lang.String featureGroup) { + this._featureGroup = featureGroup; + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setOtherData( + final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) { + throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); + } + + this._otherDataList.set(index, vOtherData); + } + + /** + * + * + * @param vOtherDataArray + */ + public void setOtherData( + final jalview.schemabinding.version2.OtherData[] vOtherDataArray) { + //-- copy array + _otherDataList.clear(); + + for (int i = 0; i < vOtherDataArray.length; i++) { + this._otherDataList.add(vOtherDataArray[i]); + } + } + + /** + * Sets the value of field 'score'. + * + * @param score the value of field 'score'. + */ + public void setScore( + final float score) { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'status'. + * + * @param status the value of field 'status'. + */ + public void setStatus( + final java.lang.String status) { + this._status = status; + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Featur + */ + public static jalview.schemabinding.version2.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java index 5ce4054..19c567c 100755 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -1,432 +1,432 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 FeatureSettings. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettings implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _settingList. - */ - private java.util.Vector _settingList; - - /** - * Field _groupList. - */ - private java.util.Vector _groupList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeatureSettings() { - super(); - this._settingList = new java.util.Vector(); - this._groupList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addGroup( - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException { - this._groupList.addElement(vGroup); - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addGroup( - final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException { - this._groupList.add(index, vGroup); - } - - /** - * - * - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSetting( - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException { - this._settingList.addElement(vSetting); - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSetting( - final int index, - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException { - this._settingList.add(index, vSetting); - } - - /** - * Method enumerateGroup. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Group elements - */ - public java.util.Enumeration enumerateGroup( - ) { - return this._groupList.elements(); - } - - /** - * Method enumerateSetting. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Setting elements - */ - public java.util.Enumeration enumerateSetting( - ) { - return this._settingList.elements(); - } - - /** - * Method getGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Group at the given index - */ - public jalview.schemabinding.version2.Group getGroup( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) { - throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Group) _groupList.get(index); - } - - /** - * Method getGroup.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Group[] getGroup( - ) { - jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0]; - return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array); - } - - /** - * Method getGroupCount. - * - * @return the size of this collection - */ - public int getGroupCount( - ) { - return this._groupList.size(); - } - - /** - * Method getSetting. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Setting at the given index - */ - public jalview.schemabinding.version2.Setting getSetting( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) { - throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Setting) _settingList.get(index); - } - - /** - * Method getSetting.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Setting[] getSetting( - ) { - jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0]; - return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array); - } - - /** - * Method getSettingCount. - * - * @return the size of this collection - */ - public int getSettingCount( - ) { - return this._settingList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllGroup( - ) { - this._groupList.clear(); - } - - /** - */ - public void removeAllSetting( - ) { - this._settingList.clear(); - } - - /** - * Method removeGroup. - * - * @param vGroup - * @return true if the object was removed from the collection. - */ - public boolean removeGroup( - final jalview.schemabinding.version2.Group vGroup) { - boolean removed = _groupList.remove(vGroup); - return removed; - } - - /** - * Method removeGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Group removeGroupAt( - final int index) { - java.lang.Object obj = this._groupList.remove(index); - return (jalview.schemabinding.version2.Group) obj; - } - - /** - * Method removeSetting. - * - * @param vSetting - * @return true if the object was removed from the collection. - */ - public boolean removeSetting( - final jalview.schemabinding.version2.Setting vSetting) { - boolean removed = _settingList.remove(vSetting); - return removed; - } - - /** - * Method removeSettingAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Setting removeSettingAt( - final int index) { - java.lang.Object obj = this._settingList.remove(index); - return (jalview.schemabinding.version2.Setting) obj; - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setGroup( - final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) { - throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); - } - - this._groupList.set(index, vGroup); - } - - /** - * - * - * @param vGroupArray - */ - public void setGroup( - final jalview.schemabinding.version2.Group[] vGroupArray) { - //-- copy array - _groupList.clear(); - - for (int i = 0; i < vGroupArray.length; i++) { - this._groupList.add(vGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSetting( - final int index, - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) { - throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); - } - - this._settingList.set(index, vSetting); - } - - /** - * - * - * @param vSettingArray - */ - public void setSetting( - final jalview.schemabinding.version2.Setting[] vSettingArray) { - //-- copy array - _settingList.clear(); - - for (int i = 0; i < vSettingArray.length; i++) { - this._settingList.add(vSettingArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.FeatureSettings - */ - public static jalview.schemabinding.version2.FeatureSettings unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 FeatureSettings. + * + * @version $Revision$ $Date$ + */ +public class FeatureSettings implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _settingList. + */ + private java.util.Vector _settingList; + + /** + * Field _groupList. + */ + private java.util.Vector _groupList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureSettings() { + super(); + this._settingList = new java.util.Vector(); + this._groupList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addGroup( + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + this._groupList.addElement(vGroup); + } + + /** + * + * + * @param index + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addGroup( + final int index, + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + this._groupList.add(index, vGroup); + } + + /** + * + * + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSetting( + final jalview.schemabinding.version2.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + this._settingList.addElement(vSetting); + } + + /** + * + * + * @param index + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSetting( + final int index, + final jalview.schemabinding.version2.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + this._settingList.add(index, vSetting); + } + + /** + * Method enumerateGroup. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Group elements + */ + public java.util.Enumeration enumerateGroup( + ) { + return this._groupList.elements(); + } + + /** + * Method enumerateSetting. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Setting elements + */ + public java.util.Enumeration enumerateSetting( + ) { + return this._settingList.elements(); + } + + /** + * Method getGroup. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Group at the given index + */ + public jalview.schemabinding.version2.Group getGroup( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._groupList.size()) { + throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Group) _groupList.get(index); + } + + /** + * Method getGroup.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Group[] getGroup( + ) { + jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0]; + return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array); + } + + /** + * Method getGroupCount. + * + * @return the size of this collection + */ + public int getGroupCount( + ) { + return this._groupList.size(); + } + + /** + * Method getSetting. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Setting at the given index + */ + public jalview.schemabinding.version2.Setting getSetting( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._settingList.size()) { + throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Setting) _settingList.get(index); + } + + /** + * Method getSetting.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Setting[] getSetting( + ) { + jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0]; + return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array); + } + + /** + * Method getSettingCount. + * + * @return the size of this collection + */ + public int getSettingCount( + ) { + return this._settingList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllGroup( + ) { + this._groupList.clear(); + } + + /** + */ + public void removeAllSetting( + ) { + this._settingList.clear(); + } + + /** + * Method removeGroup. + * + * @param vGroup + * @return true if the object was removed from the collection. + */ + public boolean removeGroup( + final jalview.schemabinding.version2.Group vGroup) { + boolean removed = _groupList.remove(vGroup); + return removed; + } + + /** + * Method removeGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Group removeGroupAt( + final int index) { + java.lang.Object obj = this._groupList.remove(index); + return (jalview.schemabinding.version2.Group) obj; + } + + /** + * Method removeSetting. + * + * @param vSetting + * @return true if the object was removed from the collection. + */ + public boolean removeSetting( + final jalview.schemabinding.version2.Setting vSetting) { + boolean removed = _settingList.remove(vSetting); + return removed; + } + + /** + * Method removeSettingAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Setting removeSettingAt( + final int index) { + java.lang.Object obj = this._settingList.remove(index); + return (jalview.schemabinding.version2.Setting) obj; + } + + /** + * + * + * @param index + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setGroup( + final int index, + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._groupList.size()) { + throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); + } + + this._groupList.set(index, vGroup); + } + + /** + * + * + * @param vGroupArray + */ + public void setGroup( + final jalview.schemabinding.version2.Group[] vGroupArray) { + //-- copy array + _groupList.clear(); + + for (int i = 0; i < vGroupArray.length; i++) { + this._groupList.add(vGroupArray[i]); + } + } + + /** + * + * + * @param index + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSetting( + final int index, + final jalview.schemabinding.version2.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._settingList.size()) { + throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); + } + + this._settingList.set(index, vSetting); + } + + /** + * + * + * @param vSettingArray + */ + public void setSetting( + final jalview.schemabinding.version2.Setting[] vSettingArray) { + //-- copy array + _settingList.clear(); + + for (int i = 0; i < vSettingArray.length; i++) { + this._settingList.add(vSettingArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.FeatureSettings + */ + public static jalview.schemabinding.version2.FeatureSettings unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java index 47b28a3..f0c5ad5 100755 --- a/src/jalview/schemabinding/version2/Features.java +++ b/src/jalview/schemabinding/version2/Features.java @@ -1,116 +1,116 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Features. - * - * @version $Revision$ $Date$ - */ -public class Features extends Feature -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Features() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Features. + * + * @version $Revision$ $Date$ + */ +public class Features extends Feature +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Features() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Featur + */ + public static jalview.schemabinding.version2.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java index 826667e..774321b 100644 --- a/src/jalview/schemabinding/version2/Group.java +++ b/src/jalview/schemabinding/version2/Group.java @@ -1,202 +1,202 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Group. - * - * @version $Revision$ $Date$ - */ -public class Group implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Group() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteDisplay( - ) { - this._has_display= false; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay( - ) { - return this._display; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName( - ) { - return this._name; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay( - ) { - return this._has_display; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay( - ) { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'display'. - * - * @param display the value of field 'display'. - */ - public void setDisplay( - final boolean display) { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName( - final java.lang.String name) { - this._name = name; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Group - */ - public static jalview.schemabinding.version2.Group unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Group. + * + * @version $Revision$ $Date$ + */ +public class Group implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _display. + */ + private boolean _display; + + /** + * keeps track of state for field: _display + */ + private boolean _has_display; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Group() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteDisplay( + ) { + this._has_display= false; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean getDisplay( + ) { + return this._display; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Method hasDisplay. + * + * @return true if at least one Display has been added + */ + public boolean hasDisplay( + ) { + return this._has_display; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean isDisplay( + ) { + return this._display; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'display'. + * + * @param display the value of field 'display'. + */ + public void setDisplay( + final boolean display) { + this._display = display; + this._has_display = true; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Group + */ + public static jalview.schemabinding.version2.Group unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java index 716bfbc..f65c9de 100644 --- a/src/jalview/schemabinding/version2/HiddenColumns.java +++ b/src/jalview/schemabinding/version2/HiddenColumns.java @@ -1,216 +1,216 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 HiddenColumns. - * - * @version $Revision$ $Date$ - */ -public class HiddenColumns implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public HiddenColumns() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteStart( - ) { - this._has_start= false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart( - ) { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart( - final int start) { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.HiddenColumns - */ - public static jalview.schemabinding.version2.HiddenColumns unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 HiddenColumns. + * + * @version $Revision$ $Date$ + */ +public class HiddenColumns implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public HiddenColumns() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.HiddenColumns + */ + public static jalview.schemabinding.version2.HiddenColumns unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index 309e704..fda1802 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -1,1150 +1,1150 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 JGroup. - * - * @version $Revision$ $Date$ - */ -public class JGroup implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _colour. - */ - private java.lang.String _colour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _outlineColour. - */ - private int _outlineColour; - - /** - * keeps track of state for field: _outlineColour - */ - private boolean _has_outlineColour; - - /** - * Field _displayBoxes. - */ - private boolean _displayBoxes; - - /** - * keeps track of state for field: _displayBoxes - */ - private boolean _has_displayBoxes; - - /** - * Field _displayText. - */ - private boolean _displayText; - - /** - * keeps track of state for field: _displayText - */ - private boolean _has_displayText; - - /** - * Field _colourText. - */ - private boolean _colourText; - - /** - * keeps track of state for field: _colourText - */ - private boolean _has_colourText; - - /** - * Field _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * Field _showUnconserved. - */ - private boolean _showUnconserved; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Optional sequence group ID (only needs to be unique for this - * alignment) - * - */ - private java.lang.String _id; - - /** - * Field _seqList. - */ - private java.util.Vector _seqList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JGroup() { - super(); - this._seqList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSeq( - final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException { - this._seqList.addElement(vSeq); - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSeq( - final int index, - final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException { - this._seqList.add(index, vSeq); - } - - /** - */ - public void deleteColourText( - ) { - this._has_colourText= false; - } - - /** - */ - public void deleteConsThreshold( - ) { - this._has_consThreshold= false; - } - - /** - */ - public void deleteDisplayBoxes( - ) { - this._has_displayBoxes= false; - } - - /** - */ - public void deleteDisplayText( - ) { - this._has_displayText= false; - } - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteIgnoreGapsinConsensus( - ) { - this._has_ignoreGapsinConsensus= false; - } - - /** - */ - public void deleteOutlineColour( - ) { - this._has_outlineColour= false; - } - - /** - */ - public void deletePidThreshold( - ) { - this._has_pidThreshold= false; - } - - /** - */ - public void deleteShowConsensusHistogram( - ) { - this._has_showConsensusHistogram= false; - } - - /** - */ - public void deleteShowSequenceLogo( - ) { - this._has_showSequenceLogo= false; - } - - /** - */ - public void deleteShowUnconserved( - ) { - this._has_showUnconserved= false; - } - - /** - */ - public void deleteStart( - ) { - this._has_start= false; - } - - /** - */ - public void deleteTextCol1( - ) { - this._has_textCol1= false; - } - - /** - */ - public void deleteTextCol2( - ) { - this._has_textCol2= false; - } - - /** - */ - public void deleteTextColThreshold( - ) { - this._has_textColThreshold= false; - } - - /** - * Method enumerateSeq. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateSeq( - ) { - return this._seqList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public java.lang.String getColour( - ) { - return this._colour; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean getColourText( - ) { - return this._colourText; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold( - ) { - return this._consThreshold; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean getDisplayBoxes( - ) { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean getDisplayText( - ) { - return this._displayText; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Optional sequence group ID (only - * needs to be unique for this alignment) - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus( - ) { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName( - ) { - return this._name; - } - - /** - * Returns the value of field 'outlineColour'. - * - * @return the value of field 'OutlineColour'. - */ - public int getOutlineColour( - ) { - return this._outlineColour; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold( - ) { - return this._pidThreshold; - } - - /** - * Method getSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getSeq( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) { - throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - return (java.lang.String) _seqList.get(index); - } - - /** - * Method getSeq.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getSeq( - ) { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._seqList.toArray(array); - } - - /** - * Method getSeqCount. - * - * @return the size of this collection - */ - public int getSeqCount( - ) { - return this._seqList.size(); - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram( - ) { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo( - ) { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved( - ) { - return this._showUnconserved; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart( - ) { - return this._start; - } - - /** - * Returns the value of field 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1( - ) { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2( - ) { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold( - ) { - return this._textColThreshold; - } - - /** - * Method hasColourText. - * - * @return true if at least one ColourText has been added - */ - public boolean hasColourText( - ) { - return this._has_colourText; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold( - ) { - return this._has_consThreshold; - } - - /** - * Method hasDisplayBoxes. - * - * @return true if at least one DisplayBoxes has been added - */ - public boolean hasDisplayBoxes( - ) { - return this._has_displayBoxes; - } - - /** - * Method hasDisplayText. - * - * @return true if at least one DisplayText has been added - */ - public boolean hasDisplayText( - ) { - return this._has_displayText; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been - * added - */ - public boolean hasIgnoreGapsinConsensus( - ) { - return this._has_ignoreGapsinConsensus; - } - - /** - * Method hasOutlineColour. - * - * @return true if at least one OutlineColour has been added - */ - public boolean hasOutlineColour( - ) { - return this._has_outlineColour; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold( - ) { - return this._has_pidThreshold; - } - - /** - * Method hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been - * added - */ - public boolean hasShowConsensusHistogram( - ) { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo( - ) { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved( - ) { - return this._has_showUnconserved; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Method hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1( - ) { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2( - ) { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold( - ) { - return this._has_textColThreshold; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean isColourText( - ) { - return this._colourText; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean isDisplayBoxes( - ) { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean isDisplayText( - ) { - return this._displayText; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus( - ) { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram( - ) { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo( - ) { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved( - ) { - return this._showUnconserved; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSeq( - ) { - this._seqList.clear(); - } - - /** - * Method removeSeq. - * - * @param vSeq - * @return true if the object was removed from the collection. - */ - public boolean removeSeq( - final java.lang.String vSeq) { - boolean removed = _seqList.remove(vSeq); - return removed; - } - - /** - * Method removeSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeSeqAt( - final int index) { - java.lang.Object obj = this._seqList.remove(index); - return (java.lang.String) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour( - final java.lang.String colour) { - this._colour = colour; - } - - /** - * Sets the value of field 'colourText'. - * - * @param colourText the value of field 'colourText'. - */ - public void setColourText( - final boolean colourText) { - this._colourText = colourText; - this._has_colourText = true; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold the value of field 'consThreshold'. - */ - public void setConsThreshold( - final int consThreshold) { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'displayBoxes'. - * - * @param displayBoxes the value of field 'displayBoxes'. - */ - public void setDisplayBoxes( - final boolean displayBoxes) { - this._displayBoxes = displayBoxes; - this._has_displayBoxes = true; - } - - /** - * Sets the value of field 'displayText'. - * - * @param displayText the value of field 'displayText'. - */ - public void setDisplayText( - final boolean displayText) { - this._displayText = displayText; - this._has_displayText = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Optional sequence group ID (only - * needs to be unique for this alignment) - * - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus the value of field - * 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus( - final boolean ignoreGapsinConsensus) { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName( - final java.lang.String name) { - this._name = name; - } - - /** - * Sets the value of field 'outlineColour'. - * - * @param outlineColour the value of field 'outlineColour'. - */ - public void setOutlineColour( - final int outlineColour) { - this._outlineColour = outlineColour; - this._has_outlineColour = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold the value of field 'pidThreshold'. - */ - public void setPidThreshold( - final int pidThreshold) { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSeq( - final int index, - final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) { - throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - this._seqList.set(index, vSeq); - } - - /** - * - * - * @param vSeqArray - */ - public void setSeq( - final java.lang.String[] vSeqArray) { - //-- copy array - _seqList.clear(); - - for (int i = 0; i < vSeqArray.length; i++) { - this._seqList.add(vSeqArray[i]); - } - } - - /** - * Sets the value of field 'showConsensusHistogram'. - * - * @param showConsensusHistogram the value of field - * 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram( - final boolean showConsensusHistogram) { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showSequenceLogo'. - * - * @param showSequenceLogo the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo( - final boolean showSequenceLogo) { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = true; - } - - /** - * Sets the value of field 'showUnconserved'. - * - * @param showUnconserved the value of field 'showUnconserved'. - */ - public void setShowUnconserved( - final boolean showUnconserved) { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart( - final int start) { - this._start = start; - this._has_start = true; - } - - /** - * Sets the value of field 'textCol1'. - * - * @param textCol1 the value of field 'textCol1'. - */ - public void setTextCol1( - final int textCol1) { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 the value of field 'textCol2'. - */ - public void setTextCol2( - final int textCol2) { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold the value of field 'textColThreshold' - */ - public void setTextColThreshold( - final int textColThreshold) { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JGroup - */ - public static jalview.schemabinding.version2.JGroup unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 JGroup. + * + * @version $Revision$ $Date$ + */ +public class JGroup implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _colour. + */ + private java.lang.String _colour; + + /** + * Field _consThreshold. + */ + private int _consThreshold; + + /** + * keeps track of state for field: _consThreshold + */ + private boolean _has_consThreshold; + + /** + * Field _pidThreshold. + */ + private int _pidThreshold; + + /** + * keeps track of state for field: _pidThreshold + */ + private boolean _has_pidThreshold; + + /** + * Field _outlineColour. + */ + private int _outlineColour; + + /** + * keeps track of state for field: _outlineColour + */ + private boolean _has_outlineColour; + + /** + * Field _displayBoxes. + */ + private boolean _displayBoxes; + + /** + * keeps track of state for field: _displayBoxes + */ + private boolean _has_displayBoxes; + + /** + * Field _displayText. + */ + private boolean _displayText; + + /** + * keeps track of state for field: _displayText + */ + private boolean _has_displayText; + + /** + * Field _colourText. + */ + private boolean _colourText; + + /** + * keeps track of state for field: _colourText + */ + private boolean _has_colourText; + + /** + * Field _textCol1. + */ + private int _textCol1; + + /** + * keeps track of state for field: _textCol1 + */ + private boolean _has_textCol1; + + /** + * Field _textCol2. + */ + private int _textCol2; + + /** + * keeps track of state for field: _textCol2 + */ + private boolean _has_textCol2; + + /** + * Field _textColThreshold. + */ + private int _textColThreshold; + + /** + * keeps track of state for field: _textColThreshold + */ + private boolean _has_textColThreshold; + + /** + * Field _showUnconserved. + */ + private boolean _showUnconserved; + + /** + * keeps track of state for field: _showUnconserved + */ + private boolean _has_showUnconserved; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showSequenceLogo. + */ + private boolean _showSequenceLogo = false; + + /** + * keeps track of state for field: _showSequenceLogo + */ + private boolean _has_showSequenceLogo; + + /** + * Optional sequence group ID (only needs to be unique for this + * alignment) + * + */ + private java.lang.String _id; + + /** + * Field _seqList. + */ + private java.util.Vector _seqList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JGroup() { + super(); + this._seqList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeq( + final java.lang.String vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.addElement(vSeq); + } + + /** + * + * + * @param index + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeq( + final int index, + final java.lang.String vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.add(index, vSeq); + } + + /** + */ + public void deleteColourText( + ) { + this._has_colourText= false; + } + + /** + */ + public void deleteConsThreshold( + ) { + this._has_consThreshold= false; + } + + /** + */ + public void deleteDisplayBoxes( + ) { + this._has_displayBoxes= false; + } + + /** + */ + public void deleteDisplayText( + ) { + this._has_displayText= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ + public void deleteOutlineColour( + ) { + this._has_outlineColour= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowSequenceLogo( + ) { + this._has_showSequenceLogo= false; + } + + /** + */ + public void deleteShowUnconserved( + ) { + this._has_showUnconserved= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + */ + public void deleteTextCol1( + ) { + this._has_textCol1= false; + } + + /** + */ + public void deleteTextCol2( + ) { + this._has_textCol2= false; + } + + /** + */ + public void deleteTextColThreshold( + ) { + this._has_textColThreshold= false; + } + + /** + * Method enumerateSeq. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateSeq( + ) { + return this._seqList.elements(); + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public java.lang.String getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'colourText'. + * + * @return the value of field 'ColourText'. + */ + public boolean getColourText( + ) { + return this._colourText; + } + + /** + * Returns the value of field 'consThreshold'. + * + * @return the value of field 'ConsThreshold'. + */ + public int getConsThreshold( + ) { + return this._consThreshold; + } + + /** + * Returns the value of field 'displayBoxes'. + * + * @return the value of field 'DisplayBoxes'. + */ + public boolean getDisplayBoxes( + ) { + return this._displayBoxes; + } + + /** + * Returns the value of field 'displayText'. + * + * @return the value of field 'DisplayText'. + */ + public boolean getDisplayText( + ) { + return this._displayText; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'outlineColour'. + * + * @return the value of field 'OutlineColour'. + */ + public int getOutlineColour( + ) { + return this._outlineColour; + } + + /** + * Returns the value of field 'pidThreshold'. + * + * @return the value of field 'PidThreshold'. + */ + public int getPidThreshold( + ) { + return this._pidThreshold; + } + + /** + * Method getSeq. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the java.lang.String at the given index + */ + public java.lang.String getSeq( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqList.size()) { + throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + return (java.lang.String) _seqList.get(index); + } + + /** + * Method getSeq.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public java.lang.String[] getSeq( + ) { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._seqList.toArray(array); + } + + /** + * Method getSeqCount. + * + * @return the size of this collection + */ + public int getSeqCount( + ) { + return this._seqList.size(); + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Returns the value of field 'textCol1'. + * + * @return the value of field 'TextCol1'. + */ + public int getTextCol1( + ) { + return this._textCol1; + } + + /** + * Returns the value of field 'textCol2'. + * + * @return the value of field 'TextCol2'. + */ + public int getTextCol2( + ) { + return this._textCol2; + } + + /** + * Returns the value of field 'textColThreshold'. + * + * @return the value of field 'TextColThreshold'. + */ + public int getTextColThreshold( + ) { + return this._textColThreshold; + } + + /** + * Method hasColourText. + * + * @return true if at least one ColourText has been added + */ + public boolean hasColourText( + ) { + return this._has_colourText; + } + + /** + * Method hasConsThreshold. + * + * @return true if at least one ConsThreshold has been added + */ + public boolean hasConsThreshold( + ) { + return this._has_consThreshold; + } + + /** + * Method hasDisplayBoxes. + * + * @return true if at least one DisplayBoxes has been added + */ + public boolean hasDisplayBoxes( + ) { + return this._has_displayBoxes; + } + + /** + * Method hasDisplayText. + * + * @return true if at least one DisplayText has been added + */ + public boolean hasDisplayText( + ) { + return this._has_displayText; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** + * Method hasOutlineColour. + * + * @return true if at least one OutlineColour has been added + */ + public boolean hasOutlineColour( + ) { + return this._has_outlineColour; + } + + /** + * Method hasPidThreshold. + * + * @return true if at least one PidThreshold has been added + */ + public boolean hasPidThreshold( + ) { + return this._has_pidThreshold; + } + + /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo( + ) { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved( + ) { + return this._has_showUnconserved; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method hasTextCol1. + * + * @return true if at least one TextCol1 has been added + */ + public boolean hasTextCol1( + ) { + return this._has_textCol1; + } + + /** + * Method hasTextCol2. + * + * @return true if at least one TextCol2 has been added + */ + public boolean hasTextCol2( + ) { + return this._has_textCol2; + } + + /** + * Method hasTextColThreshold. + * + * @return true if at least one TextColThreshold has been added + */ + public boolean hasTextColThreshold( + ) { + return this._has_textColThreshold; + } + + /** + * Returns the value of field 'colourText'. + * + * @return the value of field 'ColourText'. + */ + public boolean isColourText( + ) { + return this._colourText; + } + + /** + * Returns the value of field 'displayBoxes'. + * + * @return the value of field 'DisplayBoxes'. + */ + public boolean isDisplayBoxes( + ) { + return this._displayBoxes; + } + + /** + * Returns the value of field 'displayText'. + * + * @return the value of field 'DisplayText'. + */ + public boolean isDisplayText( + ) { + return this._displayText; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllSeq( + ) { + this._seqList.clear(); + } + + /** + * Method removeSeq. + * + * @param vSeq + * @return true if the object was removed from the collection. + */ + public boolean removeSeq( + final java.lang.String vSeq) { + boolean removed = _seqList.remove(vSeq); + return removed; + } + + /** + * Method removeSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeSeqAt( + final int index) { + java.lang.Object obj = this._seqList.remove(index); + return (java.lang.String) obj; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final java.lang.String colour) { + this._colour = colour; + } + + /** + * Sets the value of field 'colourText'. + * + * @param colourText the value of field 'colourText'. + */ + public void setColourText( + final boolean colourText) { + this._colourText = colourText; + this._has_colourText = true; + } + + /** + * Sets the value of field 'consThreshold'. + * + * @param consThreshold the value of field 'consThreshold'. + */ + public void setConsThreshold( + final int consThreshold) { + this._consThreshold = consThreshold; + this._has_consThreshold = true; + } + + /** + * Sets the value of field 'displayBoxes'. + * + * @param displayBoxes the value of field 'displayBoxes'. + */ + public void setDisplayBoxes( + final boolean displayBoxes) { + this._displayBoxes = displayBoxes; + this._has_displayBoxes = true; + } + + /** + * Sets the value of field 'displayText'. + * + * @param displayText the value of field 'displayText'. + */ + public void setDisplayText( + final boolean displayText) { + this._displayText = displayText; + this._has_displayText = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'outlineColour'. + * + * @param outlineColour the value of field 'outlineColour'. + */ + public void setOutlineColour( + final int outlineColour) { + this._outlineColour = outlineColour; + this._has_outlineColour = true; + } + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold the value of field 'pidThreshold'. + */ + public void setPidThreshold( + final int pidThreshold) { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } + + /** + * + * + * @param index + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSeq( + final int index, + final java.lang.String vSeq) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqList.size()) { + throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + this._seqList.set(index, vSeq); + } + + /** + * + * + * @param vSeqArray + */ + public void setSeq( + final java.lang.String[] vSeqArray) { + //-- copy array + _seqList.clear(); + + for (int i = 0; i < vSeqArray.length; i++) { + this._seqList.add(vSeqArray[i]); + } + } + + /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showSequenceLogo'. + * + * @param showSequenceLogo the value of field 'showSequenceLogo' + */ + public void setShowSequenceLogo( + final boolean showSequenceLogo) { + this._showSequenceLogo = showSequenceLogo; + this._has_showSequenceLogo = true; + } + + /** + * Sets the value of field 'showUnconserved'. + * + * @param showUnconserved the value of field 'showUnconserved'. + */ + public void setShowUnconserved( + final boolean showUnconserved) { + this._showUnconserved = showUnconserved; + this._has_showUnconserved = true; + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Sets the value of field 'textCol1'. + * + * @param textCol1 the value of field 'textCol1'. + */ + public void setTextCol1( + final int textCol1) { + this._textCol1 = textCol1; + this._has_textCol1 = true; + } + + /** + * Sets the value of field 'textCol2'. + * + * @param textCol2 the value of field 'textCol2'. + */ + public void setTextCol2( + final int textCol2) { + this._textCol2 = textCol2; + this._has_textCol2 = true; + } + + /** + * Sets the value of field 'textColThreshold'. + * + * @param textColThreshold the value of field 'textColThreshold' + */ + public void setTextColThreshold( + final int textColThreshold) { + this._textColThreshold = textColThreshold; + this._has_textColThreshold = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.JGroup + */ + public static jalview.schemabinding.version2.JGroup unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java index a5dc2f7..d5eda07 100755 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,814 +1,814 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 JSeq. - * - * @version $Revision$ $Date$ - */ -public class JSeq implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _hidden. - */ - private boolean _hidden; - - /** - * keeps track of state for field: _hidden - */ - private boolean _has_hidden; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - /** - * Field _hiddenSequencesList. - */ - private java.util.Vector _hiddenSequencesList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JSeq() { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - this._hiddenSequencesList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addFeatures( - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException { - this._featuresList.addElement(vFeatures); - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addFeatures( - final int index, - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addHiddenSequences( - final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException { - this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences)); - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addHiddenSequences( - final int index, - final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException { - this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences)); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addPdbids( - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException { - this._pdbidsList.addElement(vPdbids); - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addPdbids( - final int index, - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException { - this._pdbidsList.add(index, vPdbids); - } - - /** - */ - public void deleteColour( - ) { - this._has_colour= false; - } - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteHidden( - ) { - this._has_hidden= false; - } - - /** - */ - public void deleteStart( - ) { - this._has_start= false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Features elements - */ - public java.util.Enumeration enumerateFeatures( - ) { - return this._featuresList.elements(); - } - - /** - * Method enumerateHiddenSequences. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateHiddenSequences( - ) { - return this._hiddenSequencesList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Pdbids elements - */ - public java.util.Enumeration enumeratePdbids( - ) { - return this._pdbidsList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour( - ) { - return this._colour; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Method getFeatures. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Features at the given index - */ - public jalview.schemabinding.version2.Features getFeatures( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) { - throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Features) _featuresList.get(index); - } - - /** - * Method getFeatures.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Features[] getFeatures( - ) { - jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; - return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array); - } - - /** - * Method getFeaturesCount. - * - * @return the size of this collection - */ - public int getFeaturesCount( - ) { - return this._featuresList.size(); - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean getHidden( - ) { - return this._hidden; - } - - /** - * Method getHiddenSequences. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the int at the given index - */ - public int getHiddenSequences( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) { - throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); - } - - /** - * Method getHiddenSequences.Returns the contents of the - * collection in an Array. - * - * @return this collection as an Array - */ - public int[] getHiddenSequences( - ) { - int size = this._hiddenSequencesList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _hiddenSequencesList.iterator(); - for (int index = 0; index < size; index++) { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getHiddenSequencesCount. - * - * @return the size of this collection - */ - public int getHiddenSequencesCount( - ) { - return this._hiddenSequencesList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Method getPdbids. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Pdbids at the given index - */ - public jalview.schemabinding.version2.Pdbids getPdbids( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) { - throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index); - } - - /** - * Method getPdbids.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Pdbids[] getPdbids( - ) { - jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; - return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array); - } - - /** - * Method getPdbidsCount. - * - * @return the size of this collection - */ - public int getPdbidsCount( - ) { - return this._pdbidsList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart( - ) { - return this._start; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour( - ) { - return this._has_colour; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasHidden. - * - * @return true if at least one Hidden has been added - */ - public boolean hasHidden( - ) { - return this._has_hidden; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean isHidden( - ) { - return this._hidden; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllFeatures( - ) { - this._featuresList.clear(); - } - - /** - */ - public void removeAllHiddenSequences( - ) { - this._hiddenSequencesList.clear(); - } - - /** - */ - public void removeAllPdbids( - ) { - this._pdbidsList.clear(); - } - - /** - * Method removeFeatures. - * - * @param vFeatures - * @return true if the object was removed from the collection. - */ - public boolean removeFeatures( - final jalview.schemabinding.version2.Features vFeatures) { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Features removeFeaturesAt( - final int index) { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.schemabinding.version2.Features) obj; - } - - /** - * Method removeHiddenSequences. - * - * @param vHiddenSequences - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenSequences( - final int vHiddenSequences) { - boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences)); - return removed; - } - - /** - * Method removeHiddenSequencesAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeHiddenSequencesAt( - final int index) { - java.lang.Object obj = this._hiddenSequencesList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids( - final jalview.schemabinding.version2.Pdbids vPdbids) { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Pdbids removePdbidsAt( - final int index) { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.schemabinding.version2.Pdbids) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour( - final int colour) { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setFeatures( - final int index, - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) { - throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); - } - - this._featuresList.set(index, vFeatures); - } - - /** - * - * - * @param vFeaturesArray - */ - public void setFeatures( - final jalview.schemabinding.version2.Features[] vFeaturesArray) { - //-- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'hidden'. - * - * @param hidden the value of field 'hidden'. - */ - public void setHidden( - final boolean hidden) { - this._hidden = hidden; - this._has_hidden = true; - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setHiddenSequences( - final int index, - final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) { - throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); - } - - this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences)); - } - - /** - * - * - * @param vHiddenSequencesArray - */ - public void setHiddenSequences( - final int[] vHiddenSequencesArray) { - //-- copy array - _hiddenSequencesList.clear(); - - for (int i = 0; i < vHiddenSequencesArray.length; i++) { - this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i])); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setPdbids( - final int index, - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) { - throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); - } - - this._pdbidsList.set(index, vPdbids); - } - - /** - * - * - * @param vPdbidsArray - */ - public void setPdbids( - final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) { - //-- copy array - _pdbidsList.clear(); - - for (int i = 0; i < vPdbidsArray.length; i++) { - this._pdbidsList.add(vPdbidsArray[i]); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart( - final int start) { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JSeq - */ - public static jalview.schemabinding.version2.JSeq unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 JSeq. + * + * @version $Revision$ $Date$ + */ +public class JSeq implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _hidden. + */ + private boolean _hidden; + + /** + * keeps track of state for field: _hidden + */ + private boolean _has_hidden; + + /** + * Field _featuresList. + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList. + */ + private java.util.Vector _pdbidsList; + + /** + * Field _hiddenSequencesList. + */ + private java.util.Vector _hiddenSequencesList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeq() { + super(); + this._featuresList = new java.util.Vector(); + this._pdbidsList = new java.util.Vector(); + this._hiddenSequencesList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addFeatures( + final jalview.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.addElement(vFeatures); + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addFeatures( + final int index, + final jalview.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.add(index, vFeatures); + } + + /** + * + * + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenSequences( + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenSequences( + final int index, + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final jalview.schemabinding.version2.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + this._pdbidsList.addElement(vPdbids); + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final int index, + final jalview.schemabinding.version2.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + this._pdbidsList.add(index, vPdbids); + } + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteHidden( + ) { + this._has_hidden= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Method enumerateFeatures. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Features elements + */ + public java.util.Enumeration enumerateFeatures( + ) { + return this._featuresList.elements(); + } + + /** + * Method enumerateHiddenSequences. + * + * @return an Enumeration over all int elements + */ + public java.util.Enumeration enumerateHiddenSequences( + ) { + return this._hiddenSequencesList.elements(); + } + + /** + * Method enumeratePdbids. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Pdbids elements + */ + public java.util.Enumeration enumeratePdbids( + ) { + return this._pdbidsList.elements(); + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Method getFeatures. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Features at the given index + */ + public jalview.schemabinding.version2.Features getFeatures( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) { + throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Features) _featuresList.get(index); + } + + /** + * Method getFeatures.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Features[] getFeatures( + ) { + jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; + return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array); + } + + /** + * Method getFeaturesCount. + * + * @return the size of this collection + */ + public int getFeaturesCount( + ) { + return this._featuresList.size(); + } + + /** + * Returns the value of field 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean getHidden( + ) { + return this._hidden; + } + + /** + * Method getHiddenSequences. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the int at the given index + */ + public int getHiddenSequences( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) { + throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); + } + + return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); + } + + /** + * Method getHiddenSequences.Returns the contents of the + * collection in an Array. + * + * @return this collection as an Array + */ + public int[] getHiddenSequences( + ) { + int size = this._hiddenSequencesList.size(); + int[] array = new int[size]; + java.util.Iterator iter = _hiddenSequencesList.iterator(); + for (int index = 0; index < size; index++) { + array[index] = ((java.lang.Integer) iter.next()).intValue(); + } + return array; + } + + /** + * Method getHiddenSequencesCount. + * + * @return the size of this collection + */ + public int getHiddenSequencesCount( + ) { + return this._hiddenSequencesList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Method getPdbids. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Pdbids at the given index + */ + public jalview.schemabinding.version2.Pdbids getPdbids( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index); + } + + /** + * Method getPdbids.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Pdbids[] getPdbids( + ) { + jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; + return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array); + } + + /** + * Method getPdbidsCount. + * + * @return the size of this collection + */ + public int getPdbidsCount( + ) { + return this._pdbidsList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasHidden. + * + * @return true if at least one Hidden has been added + */ + public boolean hasHidden( + ) { + return this._has_hidden; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Returns the value of field 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean isHidden( + ) { + return this._hidden; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllFeatures( + ) { + this._featuresList.clear(); + } + + /** + */ + public void removeAllHiddenSequences( + ) { + this._hiddenSequencesList.clear(); + } + + /** + */ + public void removeAllPdbids( + ) { + this._pdbidsList.clear(); + } + + /** + * Method removeFeatures. + * + * @param vFeatures + * @return true if the object was removed from the collection. + */ + public boolean removeFeatures( + final jalview.schemabinding.version2.Features vFeatures) { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Features removeFeaturesAt( + final int index) { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.schemabinding.version2.Features) obj; + } + + /** + * Method removeHiddenSequences. + * + * @param vHiddenSequences + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenSequences( + final int vHiddenSequences) { + boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences)); + return removed; + } + + /** + * Method removeHiddenSequencesAt. + * + * @param index + * @return the element removed from the collection + */ + public int removeHiddenSequencesAt( + final int index) { + java.lang.Object obj = this._hiddenSequencesList.remove(index); + return ((java.lang.Integer) obj).intValue(); + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids( + final jalview.schemabinding.version2.Pdbids vPdbids) { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Pdbids removePdbidsAt( + final int index) { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.schemabinding.version2.Pdbids) obj; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setFeatures( + final int index, + final jalview.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) { + throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); + } + + this._featuresList.set(index, vFeatures); + } + + /** + * + * + * @param vFeaturesArray + */ + public void setFeatures( + final jalview.schemabinding.version2.Features[] vFeaturesArray) { + //-- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'hidden'. + * + * @param hidden the value of field 'hidden'. + */ + public void setHidden( + final boolean hidden) { + this._hidden = hidden; + this._has_hidden = true; + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setHiddenSequences( + final int index, + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) { + throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); + } + + this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param vHiddenSequencesArray + */ + public void setHiddenSequences( + final int[] vHiddenSequencesArray) { + //-- copy array + _hiddenSequencesList.clear(); + + for (int i = 0; i < vHiddenSequencesArray.length; i++) { + this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i])); + } + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbids( + final int index, + final jalview.schemabinding.version2.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + this._pdbidsList.set(index, vPdbids); + } + + /** + * + * + * @param vPdbidsArray + */ + public void setPdbids( + final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) { + //-- copy array + _pdbidsList.clear(); + + for (int i = 0; i < vPdbidsArray.length; i++) { + this._pdbidsList.add(vPdbidsArray[i]); + } + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.JSeq + */ + public static jalview.schemabinding.version2.JSeq unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java index f7e049a..eec356c 100755 --- a/src/jalview/schemabinding/version2/JalviewModel.java +++ b/src/jalview/schemabinding/version2/JalviewModel.java @@ -1,221 +1,221 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 JalviewModel. - * - * @version $Revision$ $Date$ - */ -public class JalviewModel implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _creationDate. - */ - private java.util.Date _creationDate; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _vamsasModel. - */ - private jalview.schemabinding.version2.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence. - */ - private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModel() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'creationDate'. - * - * @return the value of field 'CreationDate'. - */ - public java.util.Date getCreationDate( - ) { - return this._creationDate; - } - - /** - * Returns the value of field 'jalviewModelSequence'. - * - * @return the value of field 'JalviewModelSequence'. - */ - public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence( - ) { - return this._jalviewModelSequence; - } - - /** - * Returns the value of field 'vamsasModel'. - * - * @return the value of field 'VamsasModel'. - */ - public jalview.schemabinding.version2.VamsasModel getVamsasModel( - ) { - return this._vamsasModel; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion( - ) { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'creationDate'. - * - * @param creationDate the value of field 'creationDate'. - */ - public void setCreationDate( - final java.util.Date creationDate) { - this._creationDate = creationDate; - } - - /** - * Sets the value of field 'jalviewModelSequence'. - * - * @param jalviewModelSequence the value of field - * 'jalviewModelSequence'. - */ - public void setJalviewModelSequence( - final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) { - this._jalviewModelSequence = jalviewModelSequence; - } - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel the value of field 'vamsasModel'. - */ - public void setVamsasModel( - final jalview.schemabinding.version2.VamsasModel vamsasModel) { - this._vamsasModel = vamsasModel; - } - - /** - * Sets the value of field 'version'. - * - * @param version the value of field 'version'. - */ - public void setVersion( - final java.lang.String version) { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.JalviewModel - */ - public static jalview.schemabinding.version2.JalviewModel unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 JalviewModel. + * + * @version $Revision$ $Date$ + */ +public class JalviewModel implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _creationDate. + */ + private java.util.Date _creationDate; + + /** + * Field _version. + */ + private java.lang.String _version; + + /** + * Field _vamsasModel. + */ + private jalview.schemabinding.version2.VamsasModel _vamsasModel; + + /** + * Field _jalviewModelSequence. + */ + private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModel() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'creationDate'. + * + * @return the value of field 'CreationDate'. + */ + public java.util.Date getCreationDate( + ) { + return this._creationDate; + } + + /** + * Returns the value of field 'jalviewModelSequence'. + * + * @return the value of field 'JalviewModelSequence'. + */ + public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence( + ) { + return this._jalviewModelSequence; + } + + /** + * Returns the value of field 'vamsasModel'. + * + * @return the value of field 'VamsasModel'. + */ + public jalview.schemabinding.version2.VamsasModel getVamsasModel( + ) { + return this._vamsasModel; + } + + /** + * Returns the value of field 'version'. + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'creationDate'. + * + * @param creationDate the value of field 'creationDate'. + */ + public void setCreationDate( + final java.util.Date creationDate) { + this._creationDate = creationDate; + } + + /** + * Sets the value of field 'jalviewModelSequence'. + * + * @param jalviewModelSequence the value of field + * 'jalviewModelSequence'. + */ + public void setJalviewModelSequence( + final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) { + this._jalviewModelSequence = jalviewModelSequence; + } + + /** + * Sets the value of field 'vamsasModel'. + * + * @param vamsasModel the value of field 'vamsasModel'. + */ + public void setVamsasModel( + final jalview.schemabinding.version2.VamsasModel vamsasModel) { + this._vamsasModel = vamsasModel; + } + + /** + * Sets the value of field 'version'. + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.JalviewModel + */ + public static jalview.schemabinding.version2.JalviewModel unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index cb66b37..cf69934 100755 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -1,925 +1,925 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 JalviewModelSequence. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequence implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _JSeqList. - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList. - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList. - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList. - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _featureSettings. - */ - private jalview.schemabinding.version2.FeatureSettings _featureSettings; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelSequence() { - super(); - this._JSeqList = new java.util.Vector(); - this._JGroupList = new java.util.Vector(); - this._viewportList = new java.util.Vector(); - this._userColoursList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addJGroup( - final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException { - this._JGroupList.addElement(vJGroup); - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addJGroup( - final int index, - final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException { - this._JGroupList.add(index, vJGroup); - } - - /** - * - * - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addJSeq( - final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException { - this._JSeqList.addElement(vJSeq); - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addJSeq( - final int index, - final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException { - this._JSeqList.add(index, vJSeq); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTree( - final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTree( - final int index, - final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException { - this._treeList.add(index, vTree); - } - - /** - * - * - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addUserColours( - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException { - this._userColoursList.addElement(vUserColours); - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addUserColours( - final int index, - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException { - this._userColoursList.add(index, vUserColours); - } - - /** - * - * - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addViewport( - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException { - this._viewportList.addElement(vViewport); - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addViewport( - final int index, - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException { - this._viewportList.add(index, vViewport); - } - - /** - * Method enumerateJGroup. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.JGroup elements - */ - public java.util.Enumeration enumerateJGroup( - ) { - return this._JGroupList.elements(); - } - - /** - * Method enumerateJSeq. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.JSeq elements - */ - public java.util.Enumeration enumerateJSeq( - ) { - return this._JSeqList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Tree elements - */ - public java.util.Enumeration enumerateTree( - ) { - return this._treeList.elements(); - } - - /** - * Method enumerateUserColours. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.UserColours elements - */ - public java.util.Enumeration enumerateUserColours( - ) { - return this._userColoursList.elements(); - } - - /** - * Method enumerateViewport. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Viewport elements - */ - public java.util.Enumeration enumerateViewport( - ) { - return this._viewportList.elements(); - } - - /** - * Returns the value of field 'featureSettings'. - * - * @return the value of field 'FeatureSettings'. - */ - public jalview.schemabinding.version2.FeatureSettings getFeatureSettings( - ) { - return this._featureSettings; - } - - /** - * Method getJGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.JGroup at the given index - */ - public jalview.schemabinding.version2.JGroup getJGroup( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index); - } - - /** - * Method getJGroup.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.JGroup[] getJGroup( - ) { - jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; - return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array); - } - - /** - * Method getJGroupCount. - * - * @return the size of this collection - */ - public int getJGroupCount( - ) { - return this._JGroupList.size(); - } - - /** - * Method getJSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.JSeq - * at the given index - */ - public jalview.schemabinding.version2.JSeq getJSeq( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); - } - - /** - * Method getJSeq.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.JSeq[] getJSeq( - ) { - jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; - return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array); - } - - /** - * Method getJSeqCount. - * - * @return the size of this collection - */ - public int getJSeqCount( - ) { - return this._JSeqList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Tree - * at the given index - */ - public jalview.schemabinding.version2.Tree getTree( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Tree) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Tree[] getTree( - ) { - jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; - return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount( - ) { - return this._treeList.size(); - } - - /** - * Method getUserColours. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.UserColours at the given index - */ - public jalview.schemabinding.version2.UserColours getUserColours( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index); - } - - /** - * Method getUserColours.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.UserColours[] getUserColours( - ) { - jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; - return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array); - } - - /** - * Method getUserColoursCount. - * - * @return the size of this collection - */ - public int getUserColoursCount( - ) { - return this._userColoursList.size(); - } - - /** - * Method getViewport. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Viewport at the given index - */ - public jalview.schemabinding.version2.Viewport getViewport( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Viewport) _viewportList.get(index); - } - - /** - * Method getViewport.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Viewport[] getViewport( - ) { - jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; - return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array); - } - - /** - * Method getViewportCount. - * - * @return the size of this collection - */ - public int getViewportCount( - ) { - return this._viewportList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllJGroup( - ) { - this._JGroupList.clear(); - } - - /** - */ - public void removeAllJSeq( - ) { - this._JSeqList.clear(); - } - - /** - */ - public void removeAllTree( - ) { - this._treeList.clear(); - } - - /** - */ - public void removeAllUserColours( - ) { - this._userColoursList.clear(); - } - - /** - */ - public void removeAllViewport( - ) { - this._viewportList.clear(); - } - - /** - * Method removeJGroup. - * - * @param vJGroup - * @return true if the object was removed from the collection. - */ - public boolean removeJGroup( - final jalview.schemabinding.version2.JGroup vJGroup) { - boolean removed = _JGroupList.remove(vJGroup); - return removed; - } - - /** - * Method removeJGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JGroup removeJGroupAt( - final int index) { - java.lang.Object obj = this._JGroupList.remove(index); - return (jalview.schemabinding.version2.JGroup) obj; - } - - /** - * Method removeJSeq. - * - * @param vJSeq - * @return true if the object was removed from the collection. - */ - public boolean removeJSeq( - final jalview.schemabinding.version2.JSeq vJSeq) { - boolean removed = _JSeqList.remove(vJSeq); - return removed; - } - - /** - * Method removeJSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JSeq removeJSeqAt( - final int index) { - java.lang.Object obj = this._JSeqList.remove(index); - return (jalview.schemabinding.version2.JSeq) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree( - final jalview.schemabinding.version2.Tree vTree) { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Tree removeTreeAt( - final int index) { - java.lang.Object obj = this._treeList.remove(index); - return (jalview.schemabinding.version2.Tree) obj; - } - - /** - * Method removeUserColours. - * - * @param vUserColours - * @return true if the object was removed from the collection. - */ - public boolean removeUserColours( - final jalview.schemabinding.version2.UserColours vUserColours) { - boolean removed = _userColoursList.remove(vUserColours); - return removed; - } - - /** - * Method removeUserColoursAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.UserColours removeUserColoursAt( - final int index) { - java.lang.Object obj = this._userColoursList.remove(index); - return (jalview.schemabinding.version2.UserColours) obj; - } - - /** - * Method removeViewport. - * - * @param vViewport - * @return true if the object was removed from the collection. - */ - public boolean removeViewport( - final jalview.schemabinding.version2.Viewport vViewport) { - boolean removed = _viewportList.remove(vViewport); - return removed; - } - - /** - * Method removeViewportAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Viewport removeViewportAt( - final int index) { - java.lang.Object obj = this._viewportList.remove(index); - return (jalview.schemabinding.version2.Viewport) obj; - } - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings the value of field 'featureSettings'. - */ - public void setFeatureSettings( - final jalview.schemabinding.version2.FeatureSettings featureSettings) { - this._featureSettings = featureSettings; - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setJGroup( - final int index, - final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); - } - - this._JGroupList.set(index, vJGroup); - } - - /** - * - * - * @param vJGroupArray - */ - public void setJGroup( - final jalview.schemabinding.version2.JGroup[] vJGroupArray) { - //-- copy array - _JGroupList.clear(); - - for (int i = 0; i < vJGroupArray.length; i++) { - this._JGroupList.add(vJGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setJSeq( - final int index, - final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - this._JSeqList.set(index, vJSeq); - } - - /** - * - * - * @param vJSeqArray - */ - public void setJSeq( - final jalview.schemabinding.version2.JSeq[] vJSeqArray) { - //-- copy array - _JSeqList.clear(); - - for (int i = 0; i < vJSeqArray.length; i++) { - this._JSeqList.add(vJSeqArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setTree( - final int index, - final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree( - final jalview.schemabinding.version2.Tree[] vTreeArray) { - //-- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setUserColours( - final int index, - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); - } - - this._userColoursList.set(index, vUserColours); - } - - /** - * - * - * @param vUserColoursArray - */ - public void setUserColours( - final jalview.schemabinding.version2.UserColours[] vUserColoursArray) { - //-- copy array - _userColoursList.clear(); - - for (int i = 0; i < vUserColoursArray.length; i++) { - this._userColoursList.add(vUserColoursArray[i]); - } - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setViewport( - final int index, - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); - } - - this._viewportList.set(index, vViewport); - } - - /** - * - * - * @param vViewportArray - */ - public void setViewport( - final jalview.schemabinding.version2.Viewport[] vViewportArray) { - //-- copy array - _viewportList.clear(); - - for (int i = 0; i < vViewportArray.length; i++) { - this._viewportList.add(vViewportArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.JalviewModelSequence - */ - public static jalview.schemabinding.version2.JalviewModelSequence unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 JalviewModelSequence. + * + * @version $Revision$ $Date$ + */ +public class JalviewModelSequence implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _JSeqList. + */ + private java.util.Vector _JSeqList; + + /** + * Field _JGroupList. + */ + private java.util.Vector _JGroupList; + + /** + * Field _viewportList. + */ + private java.util.Vector _viewportList; + + /** + * Field _userColoursList. + */ + private java.util.Vector _userColoursList; + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _featureSettings. + */ + private jalview.schemabinding.version2.FeatureSettings _featureSettings; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequence() { + super(); + this._JSeqList = new java.util.Vector(); + this._JGroupList = new java.util.Vector(); + this._viewportList = new java.util.Vector(); + this._userColoursList = new java.util.Vector(); + this._treeList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJGroup( + final jalview.schemabinding.version2.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + this._JGroupList.addElement(vJGroup); + } + + /** + * + * + * @param index + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJGroup( + final int index, + final jalview.schemabinding.version2.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + this._JGroupList.add(index, vJGroup); + } + + /** + * + * + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJSeq( + final jalview.schemabinding.version2.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + this._JSeqList.addElement(vJSeq); + } + + /** + * + * + * @param index + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJSeq( + final int index, + final jalview.schemabinding.version2.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + this._JSeqList.add(index, vJSeq); + } + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final jalview.schemabinding.version2.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.addElement(vTree); + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final int index, + final jalview.schemabinding.version2.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.add(index, vTree); + } + + /** + * + * + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addUserColours( + final jalview.schemabinding.version2.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + this._userColoursList.addElement(vUserColours); + } + + /** + * + * + * @param index + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addUserColours( + final int index, + final jalview.schemabinding.version2.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + this._userColoursList.add(index, vUserColours); + } + + /** + * + * + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addViewport( + final jalview.schemabinding.version2.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + this._viewportList.addElement(vViewport); + } + + /** + * + * + * @param index + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addViewport( + final int index, + final jalview.schemabinding.version2.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + this._viewportList.add(index, vViewport); + } + + /** + * Method enumerateJGroup. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.JGroup elements + */ + public java.util.Enumeration enumerateJGroup( + ) { + return this._JGroupList.elements(); + } + + /** + * Method enumerateJSeq. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.JSeq elements + */ + public java.util.Enumeration enumerateJSeq( + ) { + return this._JSeqList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Tree elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method enumerateUserColours. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.UserColours elements + */ + public java.util.Enumeration enumerateUserColours( + ) { + return this._userColoursList.elements(); + } + + /** + * Method enumerateViewport. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Viewport elements + */ + public java.util.Enumeration enumerateViewport( + ) { + return this._viewportList.elements(); + } + + /** + * Returns the value of field 'featureSettings'. + * + * @return the value of field 'FeatureSettings'. + */ + public jalview.schemabinding.version2.FeatureSettings getFeatureSettings( + ) { + return this._featureSettings; + } + + /** + * Method getJGroup. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.JGroup at the given index + */ + public jalview.schemabinding.version2.JGroup getJGroup( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JGroupList.size()) { + throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index); + } + + /** + * Method getJGroup.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.JGroup[] getJGroup( + ) { + jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; + return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array); + } + + /** + * Method getJGroupCount. + * + * @return the size of this collection + */ + public int getJGroupCount( + ) { + return this._JGroupList.size(); + } + + /** + * Method getJSeq. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.schemabinding.version2.JSeq + * at the given index + */ + public jalview.schemabinding.version2.JSeq getJSeq( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JSeqList.size()) { + throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); + } + + /** + * Method getJSeq.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.JSeq[] getJSeq( + ) { + jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; + return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array); + } + + /** + * Method getJSeqCount. + * + * @return the size of this collection + */ + public int getJSeqCount( + ) { + return this._JSeqList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.schemabinding.version2.Tree + * at the given index + */ + public jalview.schemabinding.version2.Tree getTree( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Tree) _treeList.get(index); + } + + /** + * Method getTree.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Tree[] getTree( + ) { + jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; + return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount( + ) { + return this._treeList.size(); + } + + /** + * Method getUserColours. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.UserColours at the given index + */ + public jalview.schemabinding.version2.UserColours getUserColours( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._userColoursList.size()) { + throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index); + } + + /** + * Method getUserColours.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.UserColours[] getUserColours( + ) { + jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; + return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array); + } + + /** + * Method getUserColoursCount. + * + * @return the size of this collection + */ + public int getUserColoursCount( + ) { + return this._userColoursList.size(); + } + + /** + * Method getViewport. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Viewport at the given index + */ + public jalview.schemabinding.version2.Viewport getViewport( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._viewportList.size()) { + throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Viewport) _viewportList.get(index); + } + + /** + * Method getViewport.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Viewport[] getViewport( + ) { + jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; + return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array); + } + + /** + * Method getViewportCount. + * + * @return the size of this collection + */ + public int getViewportCount( + ) { + return this._viewportList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllJGroup( + ) { + this._JGroupList.clear(); + } + + /** + */ + public void removeAllJSeq( + ) { + this._JSeqList.clear(); + } + + /** + */ + public void removeAllTree( + ) { + this._treeList.clear(); + } + + /** + */ + public void removeAllUserColours( + ) { + this._userColoursList.clear(); + } + + /** + */ + public void removeAllViewport( + ) { + this._viewportList.clear(); + } + + /** + * Method removeJGroup. + * + * @param vJGroup + * @return true if the object was removed from the collection. + */ + public boolean removeJGroup( + final jalview.schemabinding.version2.JGroup vJGroup) { + boolean removed = _JGroupList.remove(vJGroup); + return removed; + } + + /** + * Method removeJGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.JGroup removeJGroupAt( + final int index) { + java.lang.Object obj = this._JGroupList.remove(index); + return (jalview.schemabinding.version2.JGroup) obj; + } + + /** + * Method removeJSeq. + * + * @param vJSeq + * @return true if the object was removed from the collection. + */ + public boolean removeJSeq( + final jalview.schemabinding.version2.JSeq vJSeq) { + boolean removed = _JSeqList.remove(vJSeq); + return removed; + } + + /** + * Method removeJSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.JSeq removeJSeqAt( + final int index) { + java.lang.Object obj = this._JSeqList.remove(index); + return (jalview.schemabinding.version2.JSeq) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree( + final jalview.schemabinding.version2.Tree vTree) { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Tree removeTreeAt( + final int index) { + java.lang.Object obj = this._treeList.remove(index); + return (jalview.schemabinding.version2.Tree) obj; + } + + /** + * Method removeUserColours. + * + * @param vUserColours + * @return true if the object was removed from the collection. + */ + public boolean removeUserColours( + final jalview.schemabinding.version2.UserColours vUserColours) { + boolean removed = _userColoursList.remove(vUserColours); + return removed; + } + + /** + * Method removeUserColoursAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.UserColours removeUserColoursAt( + final int index) { + java.lang.Object obj = this._userColoursList.remove(index); + return (jalview.schemabinding.version2.UserColours) obj; + } + + /** + * Method removeViewport. + * + * @param vViewport + * @return true if the object was removed from the collection. + */ + public boolean removeViewport( + final jalview.schemabinding.version2.Viewport vViewport) { + boolean removed = _viewportList.remove(vViewport); + return removed; + } + + /** + * Method removeViewportAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Viewport removeViewportAt( + final int index) { + java.lang.Object obj = this._viewportList.remove(index); + return (jalview.schemabinding.version2.Viewport) obj; + } + + /** + * Sets the value of field 'featureSettings'. + * + * @param featureSettings the value of field 'featureSettings'. + */ + public void setFeatureSettings( + final jalview.schemabinding.version2.FeatureSettings featureSettings) { + this._featureSettings = featureSettings; + } + + /** + * + * + * @param index + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setJGroup( + final int index, + final jalview.schemabinding.version2.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JGroupList.size()) { + throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); + } + + this._JGroupList.set(index, vJGroup); + } + + /** + * + * + * @param vJGroupArray + */ + public void setJGroup( + final jalview.schemabinding.version2.JGroup[] vJGroupArray) { + //-- copy array + _JGroupList.clear(); + + for (int i = 0; i < vJGroupArray.length; i++) { + this._JGroupList.add(vJGroupArray[i]); + } + } + + /** + * + * + * @param index + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setJSeq( + final int index, + final jalview.schemabinding.version2.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JSeqList.size()) { + throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + } + + this._JSeqList.set(index, vJSeq); + } + + /** + * + * + * @param vJSeqArray + */ + public void setJSeq( + final jalview.schemabinding.version2.JSeq[] vJSeqArray) { + //-- copy array + _JSeqList.clear(); + + for (int i = 0; i < vJSeqArray.length; i++) { + this._JSeqList.add(vJSeqArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setTree( + final int index, + final jalview.schemabinding.version2.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree( + final jalview.schemabinding.version2.Tree[] vTreeArray) { + //-- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) { + this._treeList.add(vTreeArray[i]); + } + } + + /** + * + * + * @param index + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setUserColours( + final int index, + final jalview.schemabinding.version2.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._userColoursList.size()) { + throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); + } + + this._userColoursList.set(index, vUserColours); + } + + /** + * + * + * @param vUserColoursArray + */ + public void setUserColours( + final jalview.schemabinding.version2.UserColours[] vUserColoursArray) { + //-- copy array + _userColoursList.clear(); + + for (int i = 0; i < vUserColoursArray.length; i++) { + this._userColoursList.add(vUserColoursArray[i]); + } + } + + /** + * + * + * @param index + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setViewport( + final int index, + final jalview.schemabinding.version2.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._viewportList.size()) { + throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); + } + + this._viewportList.set(index, vViewport); + } + + /** + * + * + * @param vViewportArray + */ + public void setViewport( + final jalview.schemabinding.version2.Viewport[] vViewportArray) { + //-- copy array + _viewportList.clear(); + + for (int i = 0; i < vViewportArray.length; i++) { + this._viewportList.add(vViewportArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.JalviewModelSequence + */ + public static jalview.schemabinding.version2.JalviewModelSequence unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java index 28541e7..e1f1a19 100755 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ b/src/jalview/schemabinding/version2/JalviewUserColours.java @@ -1,331 +1,331 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 JalviewUserColours. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColours implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * Field _colourList. - */ - private java.util.Vector _colourList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewUserColours() { - super(); - this._colourList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vColour - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addColour( - final Colour vColour) - throws java.lang.IndexOutOfBoundsException { - this._colourList.addElement(vColour); - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addColour( - final int index, - final Colour vColour) - throws java.lang.IndexOutOfBoundsException { - this._colourList.add(index, vColour); - } - - /** - * Method enumerateColour. - * - * @return an Enumeration over all Colour elements - */ - public java.util.Enumeration enumerateColour( - ) { - return this._colourList.elements(); - } - - /** - * Method getColour. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the Colour at the given index - */ - public Colour getColour( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) { - throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); - } - - return (Colour) _colourList.get(index); - } - - /** - * Method getColour.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Colour[] getColour( - ) { - Colour[] array = new Colour[0]; - return (Colour[]) this._colourList.toArray(array); - } - - /** - * Method getColourCount. - * - * @return the size of this collection - */ - public int getColourCount( - ) { - return this._colourList.size(); - } - - /** - * Returns the value of field 'schemeName'. - * - * @return the value of field 'SchemeName'. - */ - public java.lang.String getSchemeName( - ) { - return this._schemeName; - } - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Jalview colour scheme - * document version. - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion( - ) { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllColour( - ) { - this._colourList.clear(); - } - - /** - * Method removeColour. - * - * @param vColour - * @return true if the object was removed from the collection. - */ - public boolean removeColour( - final Colour vColour) { - boolean removed = _colourList.remove(vColour); - return removed; - } - - /** - * Method removeColourAt. - * - * @param index - * @return the element removed from the collection - */ - public Colour removeColourAt( - final int index) { - java.lang.Object obj = this._colourList.remove(index); - return (Colour) obj; - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setColour( - final int index, - final Colour vColour) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) { - throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); - } - - this._colourList.set(index, vColour); - } - - /** - * - * - * @param vColourArray - */ - public void setColour( - final Colour[] vColourArray) { - //-- copy array - _colourList.clear(); - - for (int i = 0; i < vColourArray.length; i++) { - this._colourList.add(vColourArray[i]); - } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName the value of field 'schemeName'. - */ - public void setSchemeName( - final java.lang.String schemeName) { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Jalview colour scheme document - * version. - * - * - * @param version the value of field 'version'. - */ - public void setVersion( - final java.lang.String version) { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 JalviewUserColours. + * + * @version $Revision$ $Date$ + */ +public class JalviewUserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _schemeName. + */ + private java.lang.String _schemeName; + + /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** + * Field _colourList. + */ + private java.util.Vector _colourList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColours() { + super(); + this._colourList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addColour( + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + this._colourList.addElement(vColour); + } + + /** + * + * + * @param index + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addColour( + final int index, + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + this._colourList.add(index, vColour); + } + + /** + * Method enumerateColour. + * + * @return an Enumeration over all Colour elements + */ + public java.util.Enumeration enumerateColour( + ) { + return this._colourList.elements(); + } + + /** + * Method getColour. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the Colour at the given index + */ + public Colour getColour( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._colourList.size()) { + throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); + } + + return (Colour) _colourList.get(index); + } + + /** + * Method getColour.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public Colour[] getColour( + ) { + Colour[] array = new Colour[0]; + return (Colour[]) this._colourList.toArray(array); + } + + /** + * Method getColourCount. + * + * @return the size of this collection + */ + public int getColourCount( + ) { + return this._colourList.size(); + } + + /** + * Returns the value of field 'schemeName'. + * + * @return the value of field 'SchemeName'. + */ + public java.lang.String getSchemeName( + ) { + return this._schemeName; + } + + /** + * Returns the value of field 'version'. The field 'version' + * has the following description: Jalview colour scheme + * document version. + * + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllColour( + ) { + this._colourList.clear(); + } + + /** + * Method removeColour. + * + * @param vColour + * @return true if the object was removed from the collection. + */ + public boolean removeColour( + final Colour vColour) { + boolean removed = _colourList.remove(vColour); + return removed; + } + + /** + * Method removeColourAt. + * + * @param index + * @return the element removed from the collection + */ + public Colour removeColourAt( + final int index) { + java.lang.Object obj = this._colourList.remove(index); + return (Colour) obj; + } + + /** + * + * + * @param index + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setColour( + final int index, + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._colourList.size()) { + throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); + } + + this._colourList.set(index, vColour); + } + + /** + * + * + * @param vColourArray + */ + public void setColour( + final Colour[] vColourArray) { + //-- copy array + _colourList.clear(); + + for (int i = 0; i < vColourArray.length; i++) { + this._colourList.add(vColourArray[i]); + } + } + + /** + * Sets the value of field 'schemeName'. + * + * @param schemeName the value of field 'schemeName'. + */ + public void setSchemeName( + final java.lang.String schemeName) { + this._schemeName = schemeName; + } + + /** + * Sets the value of field 'version'. The field 'version' has + * the following description: Jalview colour scheme document + * version. + * + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.JalviewUserColours + */ + public static jalview.schemabinding.version2.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java index acfe18e..eaa86c2 100644 --- a/src/jalview/schemabinding/version2/MapListFrom.java +++ b/src/jalview/schemabinding/version2/MapListFrom.java @@ -1,216 +1,216 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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; - -/** - * a region from start to end inclusive - * - * @version $Revision$ $Date$ - */ -public class MapListFrom implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListFrom() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteStart( - ) { - this._has_start= false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart( - ) { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart( - final int start) { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.MapListFrom - */ - public static jalview.schemabinding.version2.MapListFrom unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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; + +/** + * a region from start to end inclusive + * + * @version $Revision$ $Date$ + */ +public class MapListFrom implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListFrom() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.MapListFrom + */ + public static jalview.schemabinding.version2.MapListFrom unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java index 8c3a7e0..c60750a 100644 --- a/src/jalview/schemabinding/version2/MapListTo.java +++ b/src/jalview/schemabinding/version2/MapListTo.java @@ -1,216 +1,216 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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; - -/** - * a region from start to end inclusive - * - * @version $Revision$ $Date$ - */ -public class MapListTo implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListTo() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteEnd( - ) { - this._has_end= false; - } - - /** - */ - public void deleteStart( - ) { - this._has_start= false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd( - ) { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart( - ) { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd( - ) { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart( - ) { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd( - final int end) { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart( - final int start) { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.MapListTo - */ - public static jalview.schemabinding.version2.MapListTo unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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; + +/** + * a region from start to end inclusive + * + * @version $Revision$ $Date$ + */ +public class MapListTo implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListTo() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.MapListTo + */ + public static jalview.schemabinding.version2.MapListTo unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index 21d56e7..3efc950 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,582 +1,582 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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; - -/** - * developed after mapRangeType from - * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - * - * This effectively represents a java.util.MapList object - * - * - * @version $Revision$ $Date$ - */ -public class MapListType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - */ - private long _mapFromUnit; - - /** - * keeps track of state for field: _mapFromUnit - */ - private boolean _has_mapFromUnit; - - /** - * number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - */ - private long _mapToUnit; - - /** - * keeps track of state for field: _mapToUnit - */ - private boolean _has_mapToUnit; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListFromList; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListToList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListType() { - super(); - this._mapListFromList = new java.util.Vector(); - this._mapListToList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException { - this._mapListFromList.addElement(vMapListFrom); - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapListFrom( - final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException { - this._mapListFromList.add(index, vMapListFrom); - } - - /** - * - * - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException { - this._mapListToList.addElement(vMapListTo); - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapListTo( - final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException { - this._mapListToList.add(index, vMapListTo); - } - - /** - */ - public void deleteMapFromUnit( - ) { - this._has_mapFromUnit= false; - } - - /** - */ - public void deleteMapToUnit( - ) { - this._has_mapToUnit= false; - } - - /** - * Method enumerateMapListFrom. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.MapListFrom elements - */ - public java.util.Enumeration enumerateMapListFrom( - ) { - return this._mapListFromList.elements(); - } - - /** - * Method enumerateMapListTo. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.MapListTo elements - */ - public java.util.Enumeration enumerateMapListTo( - ) { - return this._mapListToList.elements(); - } - - /** - * Returns the value of field 'mapFromUnit'. The field - * 'mapFromUnit' has the following description: number of - * dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @return the value of field 'MapFromUnit'. - */ - public long getMapFromUnit( - ) { - return this._mapFromUnit; - } - - /** - * Method getMapListFrom. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.MapListFrom at the given index - */ - public jalview.schemabinding.version2.MapListFrom getMapListFrom( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) { - throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index); - } - - /** - * Method getMapListFrom.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.MapListFrom[] getMapListFrom( - ) { - jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; - return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array); - } - - /** - * Method getMapListFromCount. - * - * @return the size of this collection - */ - public int getMapListFromCount( - ) { - return this._mapListFromList.size(); - } - - /** - * Method getMapListTo. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.MapListTo at the given index - */ - public jalview.schemabinding.version2.MapListTo getMapListTo( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) { - throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index); - } - - /** - * Method getMapListTo.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.MapListTo[] getMapListTo( - ) { - jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; - return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array); - } - - /** - * Method getMapListToCount. - * - * @return the size of this collection - */ - public int getMapListToCount( - ) { - return this._mapListToList.size(); - } - - /** - * Returns the value of field 'mapToUnit'. The field - * 'mapToUnit' has the following description: number of - * dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @return the value of field 'MapToUnit'. - */ - public long getMapToUnit( - ) { - return this._mapToUnit; - } - - /** - * Method hasMapFromUnit. - * - * @return true if at least one MapFromUnit has been added - */ - public boolean hasMapFromUnit( - ) { - return this._has_mapFromUnit; - } - - /** - * Method hasMapToUnit. - * - * @return true if at least one MapToUnit has been added - */ - public boolean hasMapToUnit( - ) { - return this._has_mapToUnit; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllMapListFrom( - ) { - this._mapListFromList.clear(); - } - - /** - */ - public void removeAllMapListTo( - ) { - this._mapListToList.clear(); - } - - /** - * Method removeMapListFrom. - * - * @param vMapListFrom - * @return true if the object was removed from the collection. - */ - public boolean removeMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) { - boolean removed = _mapListFromList.remove(vMapListFrom); - return removed; - } - - /** - * Method removeMapListFromAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( - final int index) { - java.lang.Object obj = this._mapListFromList.remove(index); - return (jalview.schemabinding.version2.MapListFrom) obj; - } - - /** - * Method removeMapListTo. - * - * @param vMapListTo - * @return true if the object was removed from the collection. - */ - public boolean removeMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) { - boolean removed = _mapListToList.remove(vMapListTo); - return removed; - } - - /** - * Method removeMapListToAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListTo removeMapListToAt( - final int index) { - java.lang.Object obj = this._mapListToList.remove(index); - return (jalview.schemabinding.version2.MapListTo) obj; - } - - /** - * Sets the value of field 'mapFromUnit'. The field - * 'mapFromUnit' has the following description: number of - * dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @param mapFromUnit the value of field 'mapFromUnit'. - */ - public void setMapFromUnit( - final long mapFromUnit) { - this._mapFromUnit = mapFromUnit; - this._has_mapFromUnit = true; - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMapListFrom( - final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) { - throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); - } - - this._mapListFromList.set(index, vMapListFrom); - } - - /** - * - * - * @param vMapListFromArray - */ - public void setMapListFrom( - final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) { - //-- copy array - _mapListFromList.clear(); - - for (int i = 0; i < vMapListFromArray.length; i++) { - this._mapListFromList.add(vMapListFromArray[i]); - } - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMapListTo( - final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) { - throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); - } - - this._mapListToList.set(index, vMapListTo); - } - - /** - * - * - * @param vMapListToArray - */ - public void setMapListTo( - final jalview.schemabinding.version2.MapListTo[] vMapListToArray) { - //-- copy array - _mapListToList.clear(); - - for (int i = 0; i < vMapListToArray.length; i++) { - this._mapListToList.add(vMapListToArray[i]); - } - } - - /** - * Sets the value of field 'mapToUnit'. The field 'mapToUnit' - * has the following description: number of dictionary symbol - * widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @param mapToUnit the value of field 'mapToUnit'. - */ - public void setMapToUnit( - final long mapToUnit) { - this._mapToUnit = mapToUnit; - this._has_mapToUnit = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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; + +/** + * developed after mapRangeType from + * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes + * + * This effectively represents a java.util.MapList object + * + * + * @version $Revision$ $Date$ + */ +public class MapListType implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + */ + private long _mapFromUnit; + + /** + * keeps track of state for field: _mapFromUnit + */ + private boolean _has_mapFromUnit; + + /** + * number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + */ + private long _mapToUnit; + + /** + * keeps track of state for field: _mapToUnit + */ + private boolean _has_mapToUnit; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListFromList; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListToList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListType() { + super(); + this._mapListFromList = new java.util.Vector(); + this._mapListToList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + this._mapListFromList.addElement(vMapListFrom); + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListFrom( + final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + this._mapListFromList.add(index, vMapListFrom); + } + + /** + * + * + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + this._mapListToList.addElement(vMapListTo); + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListTo( + final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + this._mapListToList.add(index, vMapListTo); + } + + /** + */ + public void deleteMapFromUnit( + ) { + this._has_mapFromUnit= false; + } + + /** + */ + public void deleteMapToUnit( + ) { + this._has_mapToUnit= false; + } + + /** + * Method enumerateMapListFrom. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.MapListFrom elements + */ + public java.util.Enumeration enumerateMapListFrom( + ) { + return this._mapListFromList.elements(); + } + + /** + * Method enumerateMapListTo. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.MapListTo elements + */ + public java.util.Enumeration enumerateMapListTo( + ) { + return this._mapListToList.elements(); + } + + /** + * Returns the value of field 'mapFromUnit'. The field + * 'mapFromUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @return the value of field 'MapFromUnit'. + */ + public long getMapFromUnit( + ) { + return this._mapFromUnit; + } + + /** + * Method getMapListFrom. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.MapListFrom at the given index + */ + public jalview.schemabinding.version2.MapListFrom getMapListFrom( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) { + throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index); + } + + /** + * Method getMapListFrom.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.MapListFrom[] getMapListFrom( + ) { + jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; + return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array); + } + + /** + * Method getMapListFromCount. + * + * @return the size of this collection + */ + public int getMapListFromCount( + ) { + return this._mapListFromList.size(); + } + + /** + * Method getMapListTo. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.MapListTo at the given index + */ + public jalview.schemabinding.version2.MapListTo getMapListTo( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) { + throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index); + } + + /** + * Method getMapListTo.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.MapListTo[] getMapListTo( + ) { + jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; + return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array); + } + + /** + * Method getMapListToCount. + * + * @return the size of this collection + */ + public int getMapListToCount( + ) { + return this._mapListToList.size(); + } + + /** + * Returns the value of field 'mapToUnit'. The field + * 'mapToUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @return the value of field 'MapToUnit'. + */ + public long getMapToUnit( + ) { + return this._mapToUnit; + } + + /** + * Method hasMapFromUnit. + * + * @return true if at least one MapFromUnit has been added + */ + public boolean hasMapFromUnit( + ) { + return this._has_mapFromUnit; + } + + /** + * Method hasMapToUnit. + * + * @return true if at least one MapToUnit has been added + */ + public boolean hasMapToUnit( + ) { + return this._has_mapToUnit; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllMapListFrom( + ) { + this._mapListFromList.clear(); + } + + /** + */ + public void removeAllMapListTo( + ) { + this._mapListToList.clear(); + } + + /** + * Method removeMapListFrom. + * + * @param vMapListFrom + * @return true if the object was removed from the collection. + */ + public boolean removeMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) { + boolean removed = _mapListFromList.remove(vMapListFrom); + return removed; + } + + /** + * Method removeMapListFromAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( + final int index) { + java.lang.Object obj = this._mapListFromList.remove(index); + return (jalview.schemabinding.version2.MapListFrom) obj; + } + + /** + * Method removeMapListTo. + * + * @param vMapListTo + * @return true if the object was removed from the collection. + */ + public boolean removeMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) { + boolean removed = _mapListToList.remove(vMapListTo); + return removed; + } + + /** + * Method removeMapListToAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListTo removeMapListToAt( + final int index) { + java.lang.Object obj = this._mapListToList.remove(index); + return (jalview.schemabinding.version2.MapListTo) obj; + } + + /** + * Sets the value of field 'mapFromUnit'. The field + * 'mapFromUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @param mapFromUnit the value of field 'mapFromUnit'. + */ + public void setMapFromUnit( + final long mapFromUnit) { + this._mapFromUnit = mapFromUnit; + this._has_mapFromUnit = true; + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setMapListFrom( + final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) { + throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); + } + + this._mapListFromList.set(index, vMapListFrom); + } + + /** + * + * + * @param vMapListFromArray + */ + public void setMapListFrom( + final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) { + //-- copy array + _mapListFromList.clear(); + + for (int i = 0; i < vMapListFromArray.length; i++) { + this._mapListFromList.add(vMapListFromArray[i]); + } + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setMapListTo( + final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) { + throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); + } + + this._mapListToList.set(index, vMapListTo); + } + + /** + * + * + * @param vMapListToArray + */ + public void setMapListTo( + final jalview.schemabinding.version2.MapListTo[] vMapListToArray) { + //-- copy array + _mapListToList.clear(); + + for (int i = 0; i < vMapListToArray.length; i++) { + this._mapListToList.add(vMapListToArray[i]); + } + } + + /** + * Sets the value of field 'mapToUnit'. The field 'mapToUnit' + * has the following description: number of dictionary symbol + * widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @param mapToUnit the value of field 'mapToUnit'. + */ + public void setMapToUnit( + final long mapToUnit) { + this._mapToUnit = mapToUnit; + this._has_mapToUnit = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.MapListType + */ + public static jalview.schemabinding.version2.MapListType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java index 8dbc12f..068fd9f 100644 --- a/src/jalview/schemabinding/version2/Mapping.java +++ b/src/jalview/schemabinding/version2/Mapping.java @@ -1,165 +1,165 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Mapping. - * - * @version $Revision$ $Date$ - */ -public class Mapping extends jalview.schemabinding.version2.MapListType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _mappingChoice. - */ - private jalview.schemabinding.version2.MappingChoice _mappingChoice; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Mapping() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'choiceValue'. The field - * 'choiceValue' has the following description: Internal choice - * value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue( - ) { - return this._choiceValue; - } - - /** - * Returns the value of field 'mappingChoice'. - * - * @return the value of field 'MappingChoice'. - */ - public jalview.schemabinding.version2.MappingChoice getMappingChoice( - ) { - return this._mappingChoice; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'mappingChoice'. - * - * @param mappingChoice the value of field 'mappingChoice'. - */ - public void setMappingChoice( - final jalview.schemabinding.version2.MappingChoice mappingChoice) { - this._mappingChoice = mappingChoice; - this._choiceValue = mappingChoice; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Mapping. + * + * @version $Revision$ $Date$ + */ +public class Mapping extends jalview.schemabinding.version2.MapListType +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Internal choice value storage + */ + private java.lang.Object _choiceValue; + + /** + * Field _mappingChoice. + */ + private jalview.schemabinding.version2.MappingChoice _mappingChoice; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Mapping() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'choiceValue'. The field + * 'choiceValue' has the following description: Internal choice + * value storage + * + * @return the value of field 'ChoiceValue'. + */ + public java.lang.Object getChoiceValue( + ) { + return this._choiceValue; + } + + /** + * Returns the value of field 'mappingChoice'. + * + * @return the value of field 'MappingChoice'. + */ + public jalview.schemabinding.version2.MappingChoice getMappingChoice( + ) { + return this._mappingChoice; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'mappingChoice'. + * + * @param mappingChoice the value of field 'mappingChoice'. + */ + public void setMappingChoice( + final jalview.schemabinding.version2.MappingChoice mappingChoice) { + this._mappingChoice = mappingChoice; + this._choiceValue = mappingChoice; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.MapListType + */ + public static jalview.schemabinding.version2.MapListType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java index 5f1930d..297ed89 100644 --- a/src/jalview/schemabinding/version2/MappingChoice.java +++ b/src/jalview/schemabinding/version2/MappingChoice.java @@ -1,170 +1,170 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 MappingChoice. - * - * @version $Revision$ $Date$ - */ -public class MappingChoice implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _sequence. - */ - private jalview.schemabinding.version2.Sequence _sequence; - - /** - * Field _dseqFor. - */ - private java.lang.String _dseqFor; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MappingChoice() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'dseqFor'. - * - * @return the value of field 'DseqFor'. - */ - public java.lang.String getDseqFor( - ) { - return this._dseqFor; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public jalview.schemabinding.version2.Sequence getSequence( - ) { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'dseqFor'. - * - * @param dseqFor the value of field 'dseqFor'. - */ - public void setDseqFor( - final java.lang.String dseqFor) { - this._dseqFor = dseqFor; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence( - final jalview.schemabinding.version2.Sequence sequence) { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.MappingChoice - */ - public static jalview.schemabinding.version2.MappingChoice unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 MappingChoice. + * + * @version $Revision$ $Date$ + */ +public class MappingChoice implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _sequence. + */ + private jalview.schemabinding.version2.Sequence _sequence; + + /** + * Field _dseqFor. + */ + private java.lang.String _dseqFor; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingChoice() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'dseqFor'. + * + * @return the value of field 'DseqFor'. + */ + public java.lang.String getDseqFor( + ) { + return this._dseqFor; + } + + /** + * Returns the value of field 'sequence'. + * + * @return the value of field 'Sequence'. + */ + public jalview.schemabinding.version2.Sequence getSequence( + ) { + return this._sequence; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'dseqFor'. + * + * @param dseqFor the value of field 'dseqFor'. + */ + public void setDseqFor( + final java.lang.String dseqFor) { + this._dseqFor = dseqFor; + } + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence( + final jalview.schemabinding.version2.Sequence sequence) { + this._sequence = sequence; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.MappingChoice + */ + public static jalview.schemabinding.version2.MappingChoice unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java index 94a5566..3cdd86e 100644 --- a/src/jalview/schemabinding/version2/OtherData.java +++ b/src/jalview/schemabinding/version2/OtherData.java @@ -1,170 +1,170 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 OtherData. - * - * @version $Revision$ $Date$ - */ -public class OtherData implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _key. - */ - private java.lang.String _key; - - /** - * Field _value. - */ - private java.lang.String _value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public OtherData() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'key'. - * - * @return the value of field 'Key'. - */ - public java.lang.String getKey( - ) { - return this._key; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue( - ) { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'key'. - * - * @param key the value of field 'key'. - */ - public void setKey( - final java.lang.String key) { - this._key = key; - } - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue( - final java.lang.String value) { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.OtherData - */ - public static jalview.schemabinding.version2.OtherData unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 OtherData. + * + * @version $Revision$ $Date$ + */ +public class OtherData implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _key. + */ + private java.lang.String _key; + + /** + * Field _value. + */ + private java.lang.String _value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public OtherData() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'key'. + * + * @return the value of field 'Key'. + */ + public java.lang.String getKey( + ) { + return this._key; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public java.lang.String getValue( + ) { + return this._value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'key'. + * + * @param key the value of field 'key'. + */ + public void setKey( + final java.lang.String key) { + this._key = key; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final java.lang.String value) { + this._value = value; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.OtherData + */ + public static jalview.schemabinding.version2.OtherData unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 6ff1819..b5acfbd 100755 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,352 +1,352 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _file. - */ - private java.lang.String _file; - - /** - * Field _items. - */ - private java.util.Vector _items; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pdbentry() { - super(); - this._items = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException { - this._items.addElement(vPdbentryItem); - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addPdbentryItem( - final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.PdbentryItem elements - */ - public java.util.Enumeration enumeratePdbentryItem( - ) { - return this._items.elements(); - } - - /** - * Returns the value of field 'file'. - * - * @return the value of field 'File'. - */ - public java.lang.String getFile( - ) { - return this._file; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Method getPdbentryItem. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.PdbentryItem at the given inde - */ - public jalview.schemabinding.version2.PdbentryItem getPdbentryItem( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._items.size()) { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem( - ) { - jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; - return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array); - } - - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount( - ) { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType( - ) { - return this._type; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllPdbentryItem( - ) { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( - final int index) { - java.lang.Object obj = this._items.remove(index); - return (jalview.schemabinding.version2.PdbentryItem) obj; - } - - /** - * Sets the value of field 'file'. - * - * @param file the value of field 'file'. - */ - public void setFile( - final java.lang.String file) { - this._file = file; - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setPdbentryItem( - final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._items.size()) { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) { - //-- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType( - final java.lang.String type) { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Pdbentry. + * + * @version $Revision$ $Date$ + */ +public class Pdbentry implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _file. + */ + private java.lang.String _file; + + /** + * Field _items. + */ + private java.util.Vector _items; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Pdbentry() { + super(); + this._items = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.addElement(vPdbentryItem); + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbentryItem( + final int index, + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.add(index, vPdbentryItem); + } + + /** + * Method enumeratePdbentryItem. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.PdbentryItem elements + */ + public java.util.Enumeration enumeratePdbentryItem( + ) { + return this._items.elements(); + } + + /** + * Returns the value of field 'file'. + * + * @return the value of field 'File'. + */ + public java.lang.String getFile( + ) { + return this._file; + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Method getPdbentryItem. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.PdbentryItem at the given inde + */ + public jalview.schemabinding.version2.PdbentryItem getPdbentryItem( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._items.size()) { + throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); + } + + /** + * Method getPdbentryItem.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem( + ) { + jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; + return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array); + } + + /** + * Method getPdbentryItemCount. + * + * @return the size of this collection + */ + public int getPdbentryItemCount( + ) { + return this._items.size(); + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllPdbentryItem( + ) { + this._items.clear(); + } + + /** + * Method removePdbentryItem. + * + * @param vPdbentryItem + * @return true if the object was removed from the collection. + */ + public boolean removePdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( + final int index) { + java.lang.Object obj = this._items.remove(index); + return (jalview.schemabinding.version2.PdbentryItem) obj; + } + + /** + * Sets the value of field 'file'. + * + * @param file the value of field 'file'. + */ + public void setFile( + final java.lang.String file) { + this._file = file; + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbentryItem( + final int index, + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._items.size()) { + throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); + } + + this._items.set(index, vPdbentryItem); + } + + /** + * + * + * @param vPdbentryItemArray + */ + public void setPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) { + //-- copy array + _items.clear(); + + for (int i = 0; i < vPdbentryItemArray.length; i++) { + this._items.add(vPdbentryItemArray[i]); + } + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.Pdbentry + */ + public static jalview.schemabinding.version2.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java index 3dbc99c..129bcc7 100755 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ b/src/jalview/schemabinding/version2/PdbentryItem.java @@ -1,192 +1,192 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -/** - * Class PdbentryItem. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItem implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbentryItem() { - super(); - this._propertyList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addProperty( - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException { - this._propertyList.addElement(vProperty); - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addProperty( - final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException { - this._propertyList.add(index, vProperty); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Property elements - */ - public java.util.Enumeration enumerateProperty( - ) { - return this._propertyList.elements(); - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Property at the given index - */ - public jalview.schemabinding.version2.Property getProperty( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) { - throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Property) _propertyList.get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Property[] getProperty( - ) { - jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; - return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount( - ) { - return this._propertyList.size(); - } - - /** - */ - public void removeAllProperty( - ) { - this._propertyList.clear(); - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty( - final jalview.schemabinding.version2.Property vProperty) { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Property removePropertyAt( - final int index) { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.schemabinding.version2.Property) obj; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setProperty( - final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) { - throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final jalview.schemabinding.version2.Property[] vPropertyArray) { - //-- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) { - this._propertyList.add(vPropertyArray[i]); - } - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + +/** + * Class PdbentryItem. + * + * @version $Revision$ $Date$ + */ +public class PdbentryItem implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _propertyList. + */ + private java.util.Vector _propertyList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryItem() { + super(); + this._propertyList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addProperty( + final jalview.schemabinding.version2.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + this._propertyList.addElement(vProperty); + } + + /** + * + * + * @param index + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addProperty( + final int index, + final jalview.schemabinding.version2.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + this._propertyList.add(index, vProperty); + } + + /** + * Method enumerateProperty. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Property elements + */ + public java.util.Enumeration enumerateProperty( + ) { + return this._propertyList.elements(); + } + + /** + * Method getProperty. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Property at the given index + */ + public jalview.schemabinding.version2.Property getProperty( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Property) _propertyList.get(index); + } + + /** + * Method getProperty.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Property[] getProperty( + ) { + jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; + return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array); + } + + /** + * Method getPropertyCount. + * + * @return the size of this collection + */ + public int getPropertyCount( + ) { + return this._propertyList.size(); + } + + /** + */ + public void removeAllProperty( + ) { + this._propertyList.clear(); + } + + /** + * Method removeProperty. + * + * @param vProperty + * @return true if the object was removed from the collection. + */ + public boolean removeProperty( + final jalview.schemabinding.version2.Property vProperty) { + boolean removed = _propertyList.remove(vProperty); + return removed; + } + + /** + * Method removePropertyAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Property removePropertyAt( + final int index) { + java.lang.Object obj = this._propertyList.remove(index); + return (jalview.schemabinding.version2.Property) obj; + } + + /** + * + * + * @param index + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setProperty( + final int index, + final jalview.schemabinding.version2.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); + } + + this._propertyList.set(index, vProperty); + } + + /** + * + * + * @param vPropertyArray + */ + public void setProperty( + final jalview.schemabinding.version2.Property[] vPropertyArray) { + //-- copy array + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); + } + } + +} diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index 04685b9..5266b99 100755 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -1,280 +1,280 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Pdbids. - * - * @version $Revision$ $Date$ - */ -public class Pdbids extends jalview.schemabinding.version2.Pdbentry -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _structureStateList. - */ - private java.util.Vector _structureStateList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pdbids() { - super(); - this._structureStateList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException { - this._structureStateList.addElement(vStructureState); - } - - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException { - this._structureStateList.add(index, vStructureState); - } - - /** - * Method enumerateStructureState. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.StructureState elements - */ - public java.util.Enumeration enumerateStructureState( - ) { - return this._structureStateList.elements(); - } - - /** - * Method getStructureState. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.StructureState at the given - * index - */ - public jalview.schemabinding.version2.StructureState getStructureState( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) { - throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index); - } - - /** - * Method getStructureState.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.StructureState[] getStructureState( - ) { - jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0]; - return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array); - } - - /** - * Method getStructureStateCount. - * - * @return the size of this collection - */ - public int getStructureStateCount( - ) { - return this._structureStateList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllStructureState( - ) { - this._structureStateList.clear(); - } - - /** - * Method removeStructureState. - * - * @param vStructureState - * @return true if the object was removed from the collection. - */ - public boolean removeStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) { - boolean removed = _structureStateList.remove(vStructureState); - return removed; - } - - /** - * Method removeStructureStateAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.StructureState removeStructureStateAt( - final int index) { - java.lang.Object obj = this._structureStateList.remove(index); - return (jalview.schemabinding.version2.StructureState) obj; - } - - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) { - throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); - } - - this._structureStateList.set(index, vStructureState); - } - - /** - * - * - * @param vStructureStateArray - */ - public void setStructureState( - final jalview.schemabinding.version2.StructureState[] vStructureStateArray) { - //-- copy array - _structureStateList.clear(); - - for (int i = 0; i < vStructureStateArray.length; i++) { - this._structureStateList.add(vStructureStateArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Pdbids. + * + * @version $Revision$ $Date$ + */ +public class Pdbids extends jalview.schemabinding.version2.Pdbentry +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _structureStateList. + */ + private java.util.Vector _structureStateList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Pdbids() { + super(); + this._structureStateList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addStructureState( + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + this._structureStateList.addElement(vStructureState); + } + + /** + * + * + * @param index + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addStructureState( + final int index, + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + this._structureStateList.add(index, vStructureState); + } + + /** + * Method enumerateStructureState. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.StructureState elements + */ + public java.util.Enumeration enumerateStructureState( + ) { + return this._structureStateList.elements(); + } + + /** + * Method getStructureState. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.StructureState at the given + * index + */ + public jalview.schemabinding.version2.StructureState getStructureState( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._structureStateList.size()) { + throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index); + } + + /** + * Method getStructureState.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.StructureState[] getStructureState( + ) { + jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0]; + return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array); + } + + /** + * Method getStructureStateCount. + * + * @return the size of this collection + */ + public int getStructureStateCount( + ) { + return this._structureStateList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllStructureState( + ) { + this._structureStateList.clear(); + } + + /** + * Method removeStructureState. + * + * @param vStructureState + * @return true if the object was removed from the collection. + */ + public boolean removeStructureState( + final jalview.schemabinding.version2.StructureState vStructureState) { + boolean removed = _structureStateList.remove(vStructureState); + return removed; + } + + /** + * Method removeStructureStateAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.StructureState removeStructureStateAt( + final int index) { + java.lang.Object obj = this._structureStateList.remove(index); + return (jalview.schemabinding.version2.StructureState) obj; + } + + /** + * + * + * @param index + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setStructureState( + final int index, + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._structureStateList.size()) { + throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); + } + + this._structureStateList.set(index, vStructureState); + } + + /** + * + * + * @param vStructureStateArray + */ + public void setStructureState( + final jalview.schemabinding.version2.StructureState[] vStructureStateArray) { + //-- copy array + _structureStateList.clear(); + + for (int i = 0; i < vStructureStateArray.length; i++) { + this._structureStateList.add(vStructureStateArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.Pdbentry + */ + public static jalview.schemabinding.version2.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader); + } + + /** + * + * + * @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); + } + +} diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java index bfc4dde..714544d 100755 --- a/src/jalview/schemabinding/version2/Property.java +++ b/src/jalview/schemabinding/version2/Property.java @@ -1,170 +1,170 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Property. - * - * @version $Revision$ $Date$ - */ -public class Property implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _value. - */ - private java.lang.String _value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Property() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName( - ) { - return this._name; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue( - ) { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName( - final java.lang.String name) { - this._name = name; - } - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue( - final java.lang.String value) { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.Property - */ - public static jalview.schemabinding.version2.Property unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Property. + * + * @version $Revision$ $Date$ + */ +public class Property implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _value. + */ + private java.lang.String _value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Property() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public java.lang.String getValue( + ) { + return this._value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final java.lang.String value) { + this._value = value; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.Property + */ + public static jalview.schemabinding.version2.Property unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index e606eeb..14137d8 100755 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,311 +1,311 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends jalview.schemabinding.version2.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * dataset sequence id for this sequence. Will be created as - * union of sequences. - * - */ - private java.lang.String _dsseqid; - - /** - * Field _DBRefList. - */ - private java.util.Vector _DBRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - this._DBRefList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDBRef( - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException { - this._DBRefList.addElement(vDBRef); - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDBRef( - final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException { - this._DBRefList.add(index, vDBRef); - } - - /** - * Method enumerateDBRef. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.DBRef elements - */ - public java.util.Enumeration enumerateDBRef( - ) { - return this._DBRefList.elements(); - } - - /** - * Method getDBRef. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.DBRef at the given index - */ - public jalview.schemabinding.version2.DBRef getDBRef( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) { - throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); - } - - /** - * Method getDBRef.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.DBRef[] getDBRef( - ) { - jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; - return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array); - } - - /** - * Method getDBRefCount. - * - * @return the size of this collection - */ - public int getDBRefCount( - ) { - return this._DBRefList.size(); - } - - /** - * Returns the value of field 'dsseqid'. The field 'dsseqid' - * has the following description: dataset sequence id for this - * sequence. Will be created as union of sequences. - * - * - * @return the value of field 'Dsseqid'. - */ - public java.lang.String getDsseqid( - ) { - return this._dsseqid; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllDBRef( - ) { - this._DBRefList.clear(); - } - - /** - * Method removeDBRef. - * - * @param vDBRef - * @return true if the object was removed from the collection. - */ - public boolean removeDBRef( - final jalview.schemabinding.version2.DBRef vDBRef) { - boolean removed = _DBRefList.remove(vDBRef); - return removed; - } - - /** - * Method removeDBRefAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.DBRef removeDBRefAt( - final int index) { - java.lang.Object obj = this._DBRefList.remove(index); - return (jalview.schemabinding.version2.DBRef) obj; - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setDBRef( - final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) { - throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); - } - - this._DBRefList.set(index, vDBRef); - } - - /** - * - * - * @param vDBRefArray - */ - public void setDBRef( - final jalview.schemabinding.version2.DBRef[] vDBRefArray) { - //-- copy array - _DBRefList.clear(); - - for (int i = 0; i < vDBRefArray.length; i++) { - this._DBRefList.add(vDBRefArray[i]); - } - } - - /** - * Sets the value of field 'dsseqid'. The field 'dsseqid' has - * the following description: dataset sequence id for this - * sequence. Will be created as union of sequences. - * - * - * @param dsseqid the value of field 'dsseqid'. - */ - public void setDsseqid( - final java.lang.String dsseqid) { - this._dsseqid = dsseqid; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Sequence. + * + * @version $Revision$ $Date$ + */ +public class Sequence extends jalview.schemabinding.version2.SequenceType +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * dataset sequence id for this sequence. Will be created as + * union of sequences. + * + */ + private java.lang.String _dsseqid; + + /** + * Field _DBRefList. + */ + private java.util.Vector _DBRefList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() { + super(); + this._DBRefList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.addElement(vDBRef); + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.add(index, vDBRef); + } + + /** + * Method enumerateDBRef. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.DBRef elements + */ + public java.util.Enumeration enumerateDBRef( + ) { + return this._DBRefList.elements(); + } + + /** + * Method getDBRef. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.DBRef at the given index + */ + public jalview.schemabinding.version2.DBRef getDBRef( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) { + throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); + } + + /** + * Method getDBRef.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.DBRef[] getDBRef( + ) { + jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; + return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array); + } + + /** + * Method getDBRefCount. + * + * @return the size of this collection + */ + public int getDBRefCount( + ) { + return this._DBRefList.size(); + } + + /** + * Returns the value of field 'dsseqid'. The field 'dsseqid' + * has the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @return the value of field 'Dsseqid'. + */ + public java.lang.String getDsseqid( + ) { + return this._dsseqid; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllDBRef( + ) { + this._DBRefList.clear(); + } + + /** + * Method removeDBRef. + * + * @param vDBRef + * @return true if the object was removed from the collection. + */ + public boolean removeDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) { + boolean removed = _DBRefList.remove(vDBRef); + return removed; + } + + /** + * Method removeDBRefAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.DBRef removeDBRefAt( + final int index) { + java.lang.Object obj = this._DBRefList.remove(index); + return (jalview.schemabinding.version2.DBRef) obj; + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) { + throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + this._DBRefList.set(index, vDBRef); + } + + /** + * + * + * @param vDBRefArray + */ + public void setDBRef( + final jalview.schemabinding.version2.DBRef[] vDBRefArray) { + //-- copy array + _DBRefList.clear(); + + for (int i = 0; i < vDBRefArray.length; i++) { + this._DBRefList.add(vDBRefArray[i]); + } + } + + /** + * Sets the value of field 'dsseqid'. The field 'dsseqid' has + * the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @param dsseqid the value of field 'dsseqid'. + */ + public void setDsseqid( + final java.lang.String dsseqid) { + this._dsseqid = dsseqid; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java index 481c37f..7b670a5 100755 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,807 +1,807 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar. - */ - private java.lang.String _gapChar; - - /** - * reference to set where jalview will gather the dataset - * sequences for all sequences in the set. - * - */ - private java.lang.String _datasetId; - - /** - * Field _sequenceList. - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList. - */ - private java.util.Vector _annotationList; - - /** - * Field _sequenceSetPropertiesList. - */ - private java.util.Vector _sequenceSetPropertiesList; - - /** - * Field _alcodonFrameList. - */ - private java.util.Vector _alcodonFrameList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSet() { - super(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - this._sequenceSetPropertiesList = new java.util.Vector(); - this._alcodonFrameList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException { - this._alcodonFrameList.addElement(vAlcodonFrame); - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException { - this._alcodonFrameList.add(index, vAlcodonFrame); - } - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException { - this._annotationList.addElement(vAnnotation); - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotation( - final int index, - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException { - this._annotationList.add(index, vAnnotation); - } - - /** - * - * - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequence( - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException { - this._sequenceList.addElement(vSequence); - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequence( - final int index, - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException { - this._sequenceList.add(index, vSequence); - } - - /** - * - * - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); - } - - /** - * Method enumerateAlcodonFrame. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AlcodonFrame elements - */ - public java.util.Enumeration enumerateAlcodonFrame( - ) { - return this._alcodonFrameList.elements(); - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Annotation elements - */ - public java.util.Enumeration enumerateAnnotation( - ) { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Sequence elements - */ - public java.util.Enumeration enumerateSequence( - ) { - return this._sequenceList.elements(); - } - - /** - * Method enumerateSequenceSetProperties. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SequenceSetProperties elements - */ - public java.util.Enumeration enumerateSequenceSetProperties( - ) { - return this._sequenceSetPropertiesList.elements(); - } - - /** - * Method getAlcodonFrame. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.AlcodonFrame at the given inde - */ - public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) { - throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index); - } - - /** - * Method getAlcodonFrame.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame( - ) { - jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; - return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array); - } - - /** - * Method getAlcodonFrameCount. - * - * @return the size of this collection - */ - public int getAlcodonFrameCount( - ) { - return this._alcodonFrameList.size(); - } - - /** - * Method getAnnotation. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Annotation at the given index - */ - public jalview.schemabinding.version2.Annotation getAnnotation( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) { - throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Annotation) _annotationList.get(index); - } - - /** - * Method getAnnotation.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Annotation[] getAnnotation( - ) { - jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; - return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array); - } - - /** - * Method getAnnotationCount. - * - * @return the size of this collection - */ - public int getAnnotationCount( - ) { - return this._annotationList.size(); - } - - /** - * Returns the value of field 'datasetId'. The field - * 'datasetId' has the following description: reference to set - * where jalview will gather the dataset sequences for all - * sequences in the set. - * - * - * @return the value of field 'DatasetId'. - */ - public java.lang.String getDatasetId( - ) { - return this._datasetId; - } - - /** - * Returns the value of field 'gapChar'. - * - * @return the value of field 'GapChar'. - */ - public java.lang.String getGapChar( - ) { - return this._gapChar; - } - - /** - * Method getSequence. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Sequence at the given index - */ - public jalview.schemabinding.version2.Sequence getSequence( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) { - throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index); - } - - /** - * Method getSequence.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Sequence[] getSequence( - ) { - jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; - return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount( - ) { - return this._sequenceList.size(); - } - - /** - * Method getSequenceSetProperties. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.SequenceSetProperties at the - * given index - */ - public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { - throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index); - } - - /** - * Method getSequenceSetProperties.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties( - ) { - jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; - return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array); - } - - /** - * Method getSequenceSetPropertiesCount. - * - * @return the size of this collection - */ - public int getSequenceSetPropertiesCount( - ) { - return this._sequenceSetPropertiesList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Method removeAlcodonFrame. - * - * @param vAlcodonFrame - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) { - boolean removed = _alcodonFrameList.remove(vAlcodonFrame); - return removed; - } - - /** - * Method removeAlcodonFrameAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( - final int index) { - java.lang.Object obj = this._alcodonFrameList.remove(index); - return (jalview.schemabinding.version2.AlcodonFrame) obj; - } - - /** - */ - public void removeAllAlcodonFrame( - ) { - this._alcodonFrameList.clear(); - } - - /** - */ - public void removeAllAnnotation( - ) { - this._annotationList.clear(); - } - - /** - */ - public void removeAllSequence( - ) { - this._sequenceList.clear(); - } - - /** - */ - public void removeAllSequenceSetProperties( - ) { - this._sequenceSetPropertiesList.clear(); - } - - /** - * Method removeAnnotation. - * - * @param vAnnotation - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) { - boolean removed = _annotationList.remove(vAnnotation); - return removed; - } - - /** - * Method removeAnnotationAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Annotation removeAnnotationAt( - final int index) { - java.lang.Object obj = this._annotationList.remove(index); - return (jalview.schemabinding.version2.Annotation) obj; - } - - /** - * Method removeSequence. - * - * @param vSequence - * @return true if the object was removed from the collection. - */ - public boolean removeSequence( - final jalview.schemabinding.version2.Sequence vSequence) { - boolean removed = _sequenceList.remove(vSequence); - return removed; - } - - /** - * Method removeSequenceAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Sequence removeSequenceAt( - final int index) { - java.lang.Object obj = this._sequenceList.remove(index); - return (jalview.schemabinding.version2.Sequence) obj; - } - - /** - * Method removeSequenceSetProperties. - * - * @param vSequenceSetProperties - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) { - boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties); - return removed; - } - - /** - * Method removeSequenceSetPropertiesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( - final int index) { - java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); - return (jalview.schemabinding.version2.SequenceSetProperties) obj; - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAlcodonFrame( - final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) { - throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); - } - - this._alcodonFrameList.set(index, vAlcodonFrame); - } - - /** - * - * - * @param vAlcodonFrameArray - */ - public void setAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) { - //-- copy array - _alcodonFrameList.clear(); - - for (int i = 0; i < vAlcodonFrameArray.length; i++) { - this._alcodonFrameList.add(vAlcodonFrameArray[i]); - } - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAnnotation( - final int index, - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) { - throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); - } - - this._annotationList.set(index, vAnnotation); - } - - /** - * - * - * @param vAnnotationArray - */ - public void setAnnotation( - final jalview.schemabinding.version2.Annotation[] vAnnotationArray) { - //-- copy array - _annotationList.clear(); - - for (int i = 0; i < vAnnotationArray.length; i++) { - this._annotationList.add(vAnnotationArray[i]); - } - } - - /** - * Sets the value of field 'datasetId'. The field 'datasetId' - * has the following description: reference to set where - * jalview will gather the dataset sequences for all sequences - * in the set. - * - * - * @param datasetId the value of field 'datasetId'. - */ - public void setDatasetId( - final java.lang.String datasetId) { - this._datasetId = datasetId; - } - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar the value of field 'gapChar'. - */ - public void setGapChar( - final java.lang.String gapChar) { - this._gapChar = gapChar; - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSequence( - final int index, - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) { - throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); - } - - this._sequenceList.set(index, vSequence); - } - - /** - * - * - * @param vSequenceArray - */ - public void setSequence( - final jalview.schemabinding.version2.Sequence[] vSequenceArray) { - //-- copy array - _sequenceList.clear(); - - for (int i = 0; i < vSequenceArray.length; i++) { - this._sequenceList.add(vSequenceArray[i]); - } - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { - throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); - } - - /** - * - * - * @param vSequenceSetPropertiesArray - */ - public void setSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) { - //-- copy array - _sequenceSetPropertiesList.clear(); - - for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) { - this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.SequenceSet - */ - public static jalview.schemabinding.version2.SequenceSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 SequenceSet. + * + * @version $Revision$ $Date$ + */ +public class SequenceSet implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _gapChar. + */ + private java.lang.String _gapChar; + + /** + * reference to set where jalview will gather the dataset + * sequences for all sequences in the set. + * + */ + private java.lang.String _datasetId; + + /** + * Field _sequenceList. + */ + private java.util.Vector _sequenceList; + + /** + * Field _annotationList. + */ + private java.util.Vector _annotationList; + + /** + * Field _sequenceSetPropertiesList. + */ + private java.util.Vector _sequenceSetPropertiesList; + + /** + * Field _alcodonFrameList. + */ + private java.util.Vector _alcodonFrameList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSet() { + super(); + this._sequenceList = new java.util.Vector(); + this._annotationList = new java.util.Vector(); + this._sequenceSetPropertiesList = new java.util.Vector(); + this._alcodonFrameList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + this._alcodonFrameList.addElement(vAlcodonFrame); + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodonFrame( + final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + this._alcodonFrameList.add(index, vAlcodonFrame); + } + + /** + * + * + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotation( + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + this._annotationList.addElement(vAnnotation); + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotation( + final int index, + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + this._annotationList.add(index, vAnnotation); + } + + /** + * + * + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequence( + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + this._sequenceList.addElement(vSequence); + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequence( + final int index, + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + this._sequenceList.add(index, vSequence); + } + + /** + * + * + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); + } + + /** + * Method enumerateAlcodonFrame. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.AlcodonFrame elements + */ + public java.util.Enumeration enumerateAlcodonFrame( + ) { + return this._alcodonFrameList.elements(); + } + + /** + * Method enumerateAnnotation. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Annotation elements + */ + public java.util.Enumeration enumerateAnnotation( + ) { + return this._annotationList.elements(); + } + + /** + * Method enumerateSequence. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Sequence elements + */ + public java.util.Enumeration enumerateSequence( + ) { + return this._sequenceList.elements(); + } + + /** + * Method enumerateSequenceSetProperties. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.SequenceSetProperties elements + */ + public java.util.Enumeration enumerateSequenceSetProperties( + ) { + return this._sequenceSetPropertiesList.elements(); + } + + /** + * Method getAlcodonFrame. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AlcodonFrame at the given inde + */ + public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) { + throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index); + } + + /** + * Method getAlcodonFrame.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame( + ) { + jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; + return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array); + } + + /** + * Method getAlcodonFrameCount. + * + * @return the size of this collection + */ + public int getAlcodonFrameCount( + ) { + return this._alcodonFrameList.size(); + } + + /** + * Method getAnnotation. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Annotation at the given index + */ + public jalview.schemabinding.version2.Annotation getAnnotation( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Annotation) _annotationList.get(index); + } + + /** + * Method getAnnotation.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Annotation[] getAnnotation( + ) { + jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; + return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array); + } + + /** + * Method getAnnotationCount. + * + * @return the size of this collection + */ + public int getAnnotationCount( + ) { + return this._annotationList.size(); + } + + /** + * Returns the value of field 'datasetId'. The field + * 'datasetId' has the following description: reference to set + * where jalview will gather the dataset sequences for all + * sequences in the set. + * + * + * @return the value of field 'DatasetId'. + */ + public java.lang.String getDatasetId( + ) { + return this._datasetId; + } + + /** + * Returns the value of field 'gapChar'. + * + * @return the value of field 'GapChar'. + */ + public java.lang.String getGapChar( + ) { + return this._gapChar; + } + + /** + * Method getSequence. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Sequence at the given index + */ + public jalview.schemabinding.version2.Sequence getSequence( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index); + } + + /** + * Method getSequence.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Sequence[] getSequence( + ) { + jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; + return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array); + } + + /** + * Method getSequenceCount. + * + * @return the size of this collection + */ + public int getSequenceCount( + ) { + return this._sequenceList.size(); + } + + /** + * Method getSequenceSetProperties. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.SequenceSetProperties at the + * given index + */ + public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index); + } + + /** + * Method getSequenceSetProperties.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties( + ) { + jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; + return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array); + } + + /** + * Method getSequenceSetPropertiesCount. + * + * @return the size of this collection + */ + public int getSequenceSetPropertiesCount( + ) { + return this._sequenceSetPropertiesList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method removeAlcodonFrame. + * + * @param vAlcodonFrame + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) { + boolean removed = _alcodonFrameList.remove(vAlcodonFrame); + return removed; + } + + /** + * Method removeAlcodonFrameAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( + final int index) { + java.lang.Object obj = this._alcodonFrameList.remove(index); + return (jalview.schemabinding.version2.AlcodonFrame) obj; + } + + /** + */ + public void removeAllAlcodonFrame( + ) { + this._alcodonFrameList.clear(); + } + + /** + */ + public void removeAllAnnotation( + ) { + this._annotationList.clear(); + } + + /** + */ + public void removeAllSequence( + ) { + this._sequenceList.clear(); + } + + /** + */ + public void removeAllSequenceSetProperties( + ) { + this._sequenceSetPropertiesList.clear(); + } + + /** + * Method removeAnnotation. + * + * @param vAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotation( + final jalview.schemabinding.version2.Annotation vAnnotation) { + boolean removed = _annotationList.remove(vAnnotation); + return removed; + } + + /** + * Method removeAnnotationAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Annotation removeAnnotationAt( + final int index) { + java.lang.Object obj = this._annotationList.remove(index); + return (jalview.schemabinding.version2.Annotation) obj; + } + + /** + * Method removeSequence. + * + * @param vSequence + * @return true if the object was removed from the collection. + */ + public boolean removeSequence( + final jalview.schemabinding.version2.Sequence vSequence) { + boolean removed = _sequenceList.remove(vSequence); + return removed; + } + + /** + * Method removeSequenceAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Sequence removeSequenceAt( + final int index) { + java.lang.Object obj = this._sequenceList.remove(index); + return (jalview.schemabinding.version2.Sequence) obj; + } + + /** + * Method removeSequenceSetProperties. + * + * @param vSequenceSetProperties + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) { + boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties); + return removed; + } + + /** + * Method removeSequenceSetPropertiesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( + final int index) { + java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); + return (jalview.schemabinding.version2.SequenceSetProperties) obj; + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodonFrame( + final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) { + throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); + } + + this._alcodonFrameList.set(index, vAlcodonFrame); + } + + /** + * + * + * @param vAlcodonFrameArray + */ + public void setAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) { + //-- copy array + _alcodonFrameList.clear(); + + for (int i = 0; i < vAlcodonFrameArray.length; i++) { + this._alcodonFrameList.add(vAlcodonFrameArray[i]); + } + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotation( + final int index, + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + this._annotationList.set(index, vAnnotation); + } + + /** + * + * + * @param vAnnotationArray + */ + public void setAnnotation( + final jalview.schemabinding.version2.Annotation[] vAnnotationArray) { + //-- copy array + _annotationList.clear(); + + for (int i = 0; i < vAnnotationArray.length; i++) { + this._annotationList.add(vAnnotationArray[i]); + } + } + + /** + * Sets the value of field 'datasetId'. The field 'datasetId' + * has the following description: reference to set where + * jalview will gather the dataset sequences for all sequences + * in the set. + * + * + * @param datasetId the value of field 'datasetId'. + */ + public void setDatasetId( + final java.lang.String datasetId) { + this._datasetId = datasetId; + } + + /** + * Sets the value of field 'gapChar'. + * + * @param gapChar the value of field 'gapChar'. + */ + public void setGapChar( + final java.lang.String gapChar) { + this._gapChar = gapChar; + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequence( + final int index, + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + this._sequenceList.set(index, vSequence); + } + + /** + * + * + * @param vSequenceArray + */ + public void setSequence( + final jalview.schemabinding.version2.Sequence[] vSequenceArray) { + //-- copy array + _sequenceList.clear(); + + for (int i = 0; i < vSequenceArray.length; i++) { + this._sequenceList.add(vSequenceArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); + } + + /** + * + * + * @param vSequenceSetPropertiesArray + */ + public void setSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) { + //-- copy array + _sequenceSetPropertiesList.clear(); + + for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) { + this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.SequenceSet + */ + public static jalview.schemabinding.version2.SequenceSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java index 0d07812..5886fbb 100755 --- a/src/jalview/schemabinding/version2/SequenceType.java +++ b/src/jalview/schemabinding/version2/SequenceType.java @@ -1,220 +1,220 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _sequence. - */ - private java.lang.String _sequence; - - /** - * Field _name. - */ - private java.lang.String _name; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription( - ) { - return this._description; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName( - ) { - return this._name; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public java.lang.String getSequence( - ) { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription( - final java.lang.String description) { - this._description = description; - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName( - final java.lang.String name) { - this._name = name; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence( - final java.lang.String sequence) { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 SequenceType. + * + * @version $Revision$ $Date$ + */ +public class SequenceType implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _sequence. + */ + private java.lang.String _sequence; + + /** + * Field _name. + */ + private java.lang.String _name; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceType() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'sequence'. + * + * @return the value of field 'Sequence'. + */ + public java.lang.String getSequence( + ) { + return this._sequence; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence( + final java.lang.String sequence) { + this._sequence = sequence; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index f4e57a9..e7ea921 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -1,666 +1,666 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Setting. - * - * @version $Revision$ $Date$ - */ -public class Setting implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - /** - * Field _order. - */ - private float _order; - - /** - * keeps track of state for field: _order - */ - private boolean _has_order; - - /** - * Optional minimum colour for graduated feature colour - */ - private int _mincolour; - - /** - * keeps track of state for field: _mincolour - */ - private boolean _has_mincolour; - - /** - * threshold value for graduated feature colour - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * threshold type for graduated feature colour - */ - private int _threshstate; - - /** - * keeps track of state for field: _threshstate - */ - private boolean _has_threshstate; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Setting() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteAutoScale( - ) { - this._has_autoScale= false; - } - - /** - */ - public void deleteColour( - ) { - this._has_colour= false; - } - - /** - */ - public void deleteColourByLabel( - ) { - this._has_colourByLabel= false; - } - - /** - */ - public void deleteDisplay( - ) { - this._has_display= false; - } - - /** - */ - public void deleteMax( - ) { - this._has_max= false; - } - - /** - */ - public void deleteMin( - ) { - this._has_min= false; - } - - /** - */ - public void deleteMincolour( - ) { - this._has_mincolour= false; - } - - /** - */ - public void deleteOrder( - ) { - this._has_order= false; - } - - /** - */ - public void deleteThreshold( - ) { - this._has_threshold= false; - } - - /** - */ - public void deleteThreshstate( - ) { - this._has_threshstate= false; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale( - ) { - return this._autoScale; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour( - ) { - return this._colour; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel( - ) { - return this._colourByLabel; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay( - ) { - return this._display; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax( - ) { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin( - ) { - return this._min; - } - - /** - * Returns the value of field 'mincolour'. The field - * 'mincolour' has the following description: Optional minimum - * colour for graduated feature colour - * - * @return the value of field 'Mincolour'. - */ - public int getMincolour( - ) { - return this._mincolour; - } - - /** - * Returns the value of field 'order'. - * - * @return the value of field 'Order'. - */ - public float getOrder( - ) { - return this._order; - } - - /** - * Returns the value of field 'threshold'. The field - * 'threshold' has the following description: threshold value - * for graduated feature colour - * - * @return the value of field 'Threshold'. - */ - public float getThreshold( - ) { - return this._threshold; - } - - /** - * Returns the value of field 'threshstate'. The field - * 'threshstate' has the following description: threshold type - * for graduated feature colour - * - * @return the value of field 'Threshstate'. - */ - public int getThreshstate( - ) { - return this._threshstate; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType( - ) { - return this._type; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale( - ) { - return this._has_autoScale; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour( - ) { - return this._has_colour; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel( - ) { - return this._has_colourByLabel; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay( - ) { - return this._has_display; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax( - ) { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin( - ) { - return this._has_min; - } - - /** - * Method hasMincolour. - * - * @return true if at least one Mincolour has been added - */ - public boolean hasMincolour( - ) { - return this._has_mincolour; - } - - /** - * Method hasOrder. - * - * @return true if at least one Order has been added - */ - public boolean hasOrder( - ) { - return this._has_order; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold( - ) { - return this._has_threshold; - } - - /** - * Method hasThreshstate. - * - * @return true if at least one Threshstate has been added - */ - public boolean hasThreshstate( - ) { - return this._has_threshstate; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale( - ) { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel( - ) { - return this._colourByLabel; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay( - ) { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale the value of field 'autoScale'. - */ - public void setAutoScale( - final boolean autoScale) { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour( - final int colour) { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel the value of field 'colourByLabel'. - */ - public void setColourByLabel( - final boolean colourByLabel) { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'display'. - * - * @param display the value of field 'display'. - */ - public void setDisplay( - final boolean display) { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max the value of field 'max'. - */ - public void setMax( - final float max) { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min the value of field 'min'. - */ - public void setMin( - final float min) { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'mincolour'. The field 'mincolour' - * has the following description: Optional minimum colour for - * graduated feature colour - * - * @param mincolour the value of field 'mincolour'. - */ - public void setMincolour( - final int mincolour) { - this._mincolour = mincolour; - this._has_mincolour = true; - } - - /** - * Sets the value of field 'order'. - * - * @param order the value of field 'order'. - */ - public void setOrder( - final float order) { - this._order = order; - this._has_order = true; - } - - /** - * Sets the value of field 'threshold'. The field 'threshold' - * has the following description: threshold value for graduated - * feature colour - * - * @param threshold the value of field 'threshold'. - */ - public void setThreshold( - final float threshold) { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'threshstate'. The field - * 'threshstate' has the following description: threshold type - * for graduated feature colour - * - * @param threshstate the value of field 'threshstate'. - */ - public void setThreshstate( - final int threshstate) { - this._threshstate = threshstate; - this._has_threshstate = true; - } - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType( - final java.lang.String type) { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Settin - */ - public static jalview.schemabinding.version2.Setting unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Setting. + * + * @version $Revision$ $Date$ + */ +public class Setting implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _display. + */ + private boolean _display; + + /** + * keeps track of state for field: _display + */ + private boolean _has_display; + + /** + * Field _order. + */ + private float _order; + + /** + * keeps track of state for field: _order + */ + private boolean _has_order; + + /** + * Optional minimum colour for graduated feature colour + */ + private int _mincolour; + + /** + * keeps track of state for field: _mincolour + */ + private boolean _has_mincolour; + + /** + * threshold value for graduated feature colour + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * threshold type for graduated feature colour + */ + private int _threshstate; + + /** + * keeps track of state for field: _threshstate + */ + private boolean _has_threshstate; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Setting() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteDisplay( + ) { + this._has_display= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteMincolour( + ) { + this._has_mincolour= false; + } + + /** + */ + public void deleteOrder( + ) { + this._has_order= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + */ + public void deleteThreshstate( + ) { + this._has_threshstate= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean getDisplay( + ) { + return this._display; + } + + /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** + * Returns the value of field 'mincolour'. The field + * 'mincolour' has the following description: Optional minimum + * colour for graduated feature colour + * + * @return the value of field 'Mincolour'. + */ + public int getMincolour( + ) { + return this._mincolour; + } + + /** + * Returns the value of field 'order'. + * + * @return the value of field 'Order'. + */ + public float getOrder( + ) { + return this._order; + } + + /** + * Returns the value of field 'threshold'. The field + * 'threshold' has the following description: threshold value + * for graduated feature colour + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Returns the value of field 'threshstate'. The field + * 'threshstate' has the following description: threshold type + * for graduated feature colour + * + * @return the value of field 'Threshstate'. + */ + public int getThreshstate( + ) { + return this._threshstate; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * Method hasDisplay. + * + * @return true if at least one Display has been added + */ + public boolean hasDisplay( + ) { + return this._has_display; + } + + /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** + * Method hasMincolour. + * + * @return true if at least one Mincolour has been added + */ + public boolean hasMincolour( + ) { + return this._has_mincolour; + } + + /** + * Method hasOrder. + * + * @return true if at least one Order has been added + */ + public boolean hasOrder( + ) { + return this._has_order; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Method hasThreshstate. + * + * @return true if at least one Threshstate has been added + */ + public boolean hasThreshstate( + ) { + return this._has_threshstate; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean isDisplay( + ) { + return this._display; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** + * Sets the value of field 'display'. + * + * @param display the value of field 'display'. + */ + public void setDisplay( + final boolean display) { + this._display = display; + this._has_display = true; + } + + /** + * Sets the value of field 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'mincolour'. The field 'mincolour' + * has the following description: Optional minimum colour for + * graduated feature colour + * + * @param mincolour the value of field 'mincolour'. + */ + public void setMincolour( + final int mincolour) { + this._mincolour = mincolour; + this._has_mincolour = true; + } + + /** + * Sets the value of field 'order'. + * + * @param order the value of field 'order'. + */ + public void setOrder( + final float order) { + this._order = order; + this._has_order = true; + } + + /** + * Sets the value of field 'threshold'. The field 'threshold' + * has the following description: threshold value for graduated + * feature colour + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Sets the value of field 'threshstate'. The field + * 'threshstate' has the following description: threshold type + * for graduated feature colour + * + * @param threshstate the value of field 'threshstate'. + */ + public void setThreshstate( + final int threshstate) { + this._threshstate = threshstate; + this._has_threshstate = true; + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Settin + */ + public static jalview.schemabinding.version2.Setting unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java index 4e3f124..31affa2 100755 --- a/src/jalview/schemabinding/version2/ThresholdLine.java +++ b/src/jalview/schemabinding/version2/ThresholdLine.java @@ -1,241 +1,241 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 ThresholdLine. - * - * @version $Revision$ $Date$ - */ -public class ThresholdLine implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ThresholdLine() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteColour( - ) { - this._has_colour= false; - } - - /** - */ - public void deleteValue( - ) { - this._has_value= false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour( - ) { - return this._colour; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel( - ) { - return this._label; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue( - ) { - return this._value; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour( - ) { - return this._has_colour; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue( - ) { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour( - final int colour) { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel( - final java.lang.String label) { - this._label = label; - } - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue( - final float value) { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.ThresholdLine - */ - public static jalview.schemabinding.version2.ThresholdLine unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 ThresholdLine. + * + * @version $Revision$ $Date$ + */ +public class ThresholdLine implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _value. + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ThresholdLine() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public float getValue( + ) { + return this._value; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasValue. + * + * @return true if at least one Value has been added + */ + public boolean hasValue( + ) { + return this._has_value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final float value) { + this._value = value; + this._has_value = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.ThresholdLine + */ + public static jalview.schemabinding.version2.ThresholdLine unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java index c73cb12..14814cc 100755 --- a/src/jalview/schemabinding/version2/Tree.java +++ b/src/jalview/schemabinding/version2/Tree.java @@ -1,852 +1,852 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _showBootstrap. - */ - private boolean _showBootstrap; - - /** - * keeps track of state for field: _showBootstrap - */ - private boolean _has_showBootstrap; - - /** - * Field _showDistances. - */ - private boolean _showDistances; - - /** - * keeps track of state for field: _showDistances - */ - private boolean _has_showDistances; - - /** - * Field _markUnlinked. - */ - private boolean _markUnlinked; - - /** - * keeps track of state for field: _markUnlinked - */ - private boolean _has_markUnlinked; - - /** - * Field _fitToWindow. - */ - private boolean _fitToWindow; - - /** - * keeps track of state for field: _fitToWindow - */ - private boolean _has_fitToWindow; - - /** - * Field _currentTree. - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; - - /** - * Tree ID added for binding tree visualization settings to - * vamsas document trees in jalview 2.4.1 - */ - private java.lang.String _id; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _newick. - */ - private java.lang.String _newick; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - */ - public void deleteCurrentTree( - ) { - this._has_currentTree= false; - } - - /** - */ - public void deleteFitToWindow( - ) { - this._has_fitToWindow= false; - } - - /** - */ - public void deleteFontSize( - ) { - this._has_fontSize= false; - } - - /** - */ - public void deleteFontStyle( - ) { - this._has_fontStyle= false; - } - - /** - */ - public void deleteHeight( - ) { - this._has_height= false; - } - - /** - */ - public void deleteMarkUnlinked( - ) { - this._has_markUnlinked= false; - } - - /** - */ - public void deleteShowBootstrap( - ) { - this._has_showBootstrap= false; - } - - /** - */ - public void deleteShowDistances( - ) { - this._has_showDistances= false; - } - - /** - */ - public void deleteThreshold( - ) { - this._has_threshold= false; - } - - /** - */ - public void deleteWidth( - ) { - this._has_width= false; - } - - /** - */ - public void deleteXpos( - ) { - this._has_xpos= false; - } - - /** - */ - public void deleteYpos( - ) { - this._has_ypos= false; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean getCurrentTree( - ) { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean getFitToWindow( - ) { - return this._fitToWindow; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName( - ) { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize( - ) { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle( - ) { - return this._fontStyle; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight( - ) { - return this._height; - } - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Tree ID added for binding tree - * visualization settings to vamsas document trees in jalview - * 2.4.1 - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean getMarkUnlinked( - ) { - return this._markUnlinked; - } - - /** - * Returns the value of field 'newick'. - * - * @return the value of field 'Newick'. - */ - public java.lang.String getNewick( - ) { - return this._newick; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean getShowBootstrap( - ) { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean getShowDistances( - ) { - return this._showDistances; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold( - ) { - return this._threshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle( - ) { - return this._title; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth( - ) { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos( - ) { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos( - ) { - return this._ypos; - } - - /** - * Method hasCurrentTree. - * - * @return true if at least one CurrentTree has been added - */ - public boolean hasCurrentTree( - ) { - return this._has_currentTree; - } - - /** - * Method hasFitToWindow. - * - * @return true if at least one FitToWindow has been added - */ - public boolean hasFitToWindow( - ) { - return this._has_fitToWindow; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize( - ) { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle( - ) { - return this._has_fontStyle; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight( - ) { - return this._has_height; - } - - /** - * Method hasMarkUnlinked. - * - * @return true if at least one MarkUnlinked has been added - */ - public boolean hasMarkUnlinked( - ) { - return this._has_markUnlinked; - } - - /** - * Method hasShowBootstrap. - * - * @return true if at least one ShowBootstrap has been added - */ - public boolean hasShowBootstrap( - ) { - return this._has_showBootstrap; - } - - /** - * Method hasShowDistances. - * - * @return true if at least one ShowDistances has been added - */ - public boolean hasShowDistances( - ) { - return this._has_showDistances; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold( - ) { - return this._has_threshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth( - ) { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos( - ) { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos( - ) { - return this._has_ypos; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean isCurrentTree( - ) { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean isFitToWindow( - ) { - return this._fitToWindow; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean isMarkUnlinked( - ) { - return this._markUnlinked; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean isShowBootstrap( - ) { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean isShowDistances( - ) { - return this._showDistances; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'currentTree'. - * - * @param currentTree the value of field 'currentTree'. - */ - public void setCurrentTree( - final boolean currentTree) { - this._currentTree = currentTree; - this._has_currentTree = true; - } - - /** - * Sets the value of field 'fitToWindow'. - * - * @param fitToWindow the value of field 'fitToWindow'. - */ - public void setFitToWindow( - final boolean fitToWindow) { - this._fitToWindow = fitToWindow; - this._has_fitToWindow = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName the value of field 'fontName'. - */ - public void setFontName( - final java.lang.String fontName) { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize the value of field 'fontSize'. - */ - public void setFontSize( - final int fontSize) { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle the value of field 'fontStyle'. - */ - public void setFontStyle( - final int fontStyle) { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height the value of field 'height'. - */ - public void setHeight( - final int height) { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Tree ID added for binding tree - * visualization settings to vamsas document trees in jalview - * 2.4.1 - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'markUnlinked'. - * - * @param markUnlinked the value of field 'markUnlinked'. - */ - public void setMarkUnlinked( - final boolean markUnlinked) { - this._markUnlinked = markUnlinked; - this._has_markUnlinked = true; - } - - /** - * Sets the value of field 'newick'. - * - * @param newick the value of field 'newick'. - */ - public void setNewick( - final java.lang.String newick) { - this._newick = newick; - } - - /** - * Sets the value of field 'showBootstrap'. - * - * @param showBootstrap the value of field 'showBootstrap'. - */ - public void setShowBootstrap( - final boolean showBootstrap) { - this._showBootstrap = showBootstrap; - this._has_showBootstrap = true; - } - - /** - * Sets the value of field 'showDistances'. - * - * @param showDistances the value of field 'showDistances'. - */ - public void setShowDistances( - final boolean showDistances) { - this._showDistances = showDistances; - this._has_showDistances = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold the value of field 'threshold'. - */ - public void setThreshold( - final float threshold) { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle( - final java.lang.String title) { - this._title = title; - } - - /** - * Sets the value of field 'width'. - * - * @param width the value of field 'width'. - */ - public void setWidth( - final int width) { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos the value of field 'xpos'. - */ - public void setXpos( - final int xpos) { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos the value of field 'ypos'. - */ - public void setYpos( - final int ypos) { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Tree - */ - public static jalview.schemabinding.version2.Tree unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Tree. + * + * @version $Revision$ $Date$ + */ +public class Tree implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _width. + */ + private int _width; + + /** + * keeps track of state for field: _width + */ + private boolean _has_width; + + /** + * Field _height. + */ + private int _height; + + /** + * keeps track of state for field: _height + */ + private boolean _has_height; + + /** + * Field _xpos. + */ + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos. + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; + + /** + * Field _fontName. + */ + private java.lang.String _fontName; + + /** + * Field _fontSize. + */ + private int _fontSize; + + /** + * keeps track of state for field: _fontSize + */ + private boolean _has_fontSize; + + /** + * Field _fontStyle. + */ + private int _fontStyle; + + /** + * keeps track of state for field: _fontStyle + */ + private boolean _has_fontStyle; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * Field _showBootstrap. + */ + private boolean _showBootstrap; + + /** + * keeps track of state for field: _showBootstrap + */ + private boolean _has_showBootstrap; + + /** + * Field _showDistances. + */ + private boolean _showDistances; + + /** + * keeps track of state for field: _showDistances + */ + private boolean _has_showDistances; + + /** + * Field _markUnlinked. + */ + private boolean _markUnlinked; + + /** + * keeps track of state for field: _markUnlinked + */ + private boolean _has_markUnlinked; + + /** + * Field _fitToWindow. + */ + private boolean _fitToWindow; + + /** + * keeps track of state for field: _fitToWindow + */ + private boolean _has_fitToWindow; + + /** + * Field _currentTree. + */ + private boolean _currentTree; + + /** + * keeps track of state for field: _currentTree + */ + private boolean _has_currentTree; + + /** + * Tree ID added for binding tree visualization settings to + * vamsas document trees in jalview 2.4.1 + */ + private java.lang.String _id; + + /** + * Field _title. + */ + private java.lang.String _title; + + /** + * Field _newick. + */ + private java.lang.String _newick; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Tree() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteCurrentTree( + ) { + this._has_currentTree= false; + } + + /** + */ + public void deleteFitToWindow( + ) { + this._has_fitToWindow= false; + } + + /** + */ + public void deleteFontSize( + ) { + this._has_fontSize= false; + } + + /** + */ + public void deleteFontStyle( + ) { + this._has_fontStyle= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deleteMarkUnlinked( + ) { + this._has_markUnlinked= false; + } + + /** + */ + public void deleteShowBootstrap( + ) { + this._has_showBootstrap= false; + } + + /** + */ + public void deleteShowDistances( + ) { + this._has_showDistances= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + */ + public void deleteWidth( + ) { + this._has_width= false; + } + + /** + */ + public void deleteXpos( + ) { + this._has_xpos= false; + } + + /** + */ + public void deleteYpos( + ) { + this._has_ypos= false; + } + + /** + * Returns the value of field 'currentTree'. + * + * @return the value of field 'CurrentTree'. + */ + public boolean getCurrentTree( + ) { + return this._currentTree; + } + + /** + * Returns the value of field 'fitToWindow'. + * + * @return the value of field 'FitToWindow'. + */ + public boolean getFitToWindow( + ) { + return this._fitToWindow; + } + + /** + * Returns the value of field 'fontName'. + * + * @return the value of field 'FontName'. + */ + public java.lang.String getFontName( + ) { + return this._fontName; + } + + /** + * Returns the value of field 'fontSize'. + * + * @return the value of field 'FontSize'. + */ + public int getFontSize( + ) { + return this._fontSize; + } + + /** + * Returns the value of field 'fontStyle'. + * + * @return the value of field 'FontStyle'. + */ + public int getFontStyle( + ) { + return this._fontStyle; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Returns the value of field 'id'. The field 'id' has the + * following description: Tree ID added for binding tree + * visualization settings to vamsas document trees in jalview + * 2.4.1 + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'markUnlinked'. + * + * @return the value of field 'MarkUnlinked'. + */ + public boolean getMarkUnlinked( + ) { + return this._markUnlinked; + } + + /** + * Returns the value of field 'newick'. + * + * @return the value of field 'Newick'. + */ + public java.lang.String getNewick( + ) { + return this._newick; + } + + /** + * Returns the value of field 'showBootstrap'. + * + * @return the value of field 'ShowBootstrap'. + */ + public boolean getShowBootstrap( + ) { + return this._showBootstrap; + } + + /** + * Returns the value of field 'showDistances'. + * + * @return the value of field 'ShowDistances'. + */ + public boolean getShowDistances( + ) { + return this._showDistances; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Returns the value of field 'title'. + * + * @return the value of field 'Title'. + */ + public java.lang.String getTitle( + ) { + return this._title; + } + + /** + * Returns the value of field 'width'. + * + * @return the value of field 'Width'. + */ + public int getWidth( + ) { + return this._width; + } + + /** + * Returns the value of field 'xpos'. + * + * @return the value of field 'Xpos'. + */ + public int getXpos( + ) { + return this._xpos; + } + + /** + * Returns the value of field 'ypos'. + * + * @return the value of field 'Ypos'. + */ + public int getYpos( + ) { + return this._ypos; + } + + /** + * Method hasCurrentTree. + * + * @return true if at least one CurrentTree has been added + */ + public boolean hasCurrentTree( + ) { + return this._has_currentTree; + } + + /** + * Method hasFitToWindow. + * + * @return true if at least one FitToWindow has been added + */ + public boolean hasFitToWindow( + ) { + return this._has_fitToWindow; + } + + /** + * Method hasFontSize. + * + * @return true if at least one FontSize has been added + */ + public boolean hasFontSize( + ) { + return this._has_fontSize; + } + + /** + * Method hasFontStyle. + * + * @return true if at least one FontStyle has been added + */ + public boolean hasFontStyle( + ) { + return this._has_fontStyle; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasMarkUnlinked. + * + * @return true if at least one MarkUnlinked has been added + */ + public boolean hasMarkUnlinked( + ) { + return this._has_markUnlinked; + } + + /** + * Method hasShowBootstrap. + * + * @return true if at least one ShowBootstrap has been added + */ + public boolean hasShowBootstrap( + ) { + return this._has_showBootstrap; + } + + /** + * Method hasShowDistances. + * + * @return true if at least one ShowDistances has been added + */ + public boolean hasShowDistances( + ) { + return this._has_showDistances; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Method hasWidth. + * + * @return true if at least one Width has been added + */ + public boolean hasWidth( + ) { + return this._has_width; + } + + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added + */ + public boolean hasXpos( + ) { + return this._has_xpos; + } + + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added + */ + public boolean hasYpos( + ) { + return this._has_ypos; + } + + /** + * Returns the value of field 'currentTree'. + * + * @return the value of field 'CurrentTree'. + */ + public boolean isCurrentTree( + ) { + return this._currentTree; + } + + /** + * Returns the value of field 'fitToWindow'. + * + * @return the value of field 'FitToWindow'. + */ + public boolean isFitToWindow( + ) { + return this._fitToWindow; + } + + /** + * Returns the value of field 'markUnlinked'. + * + * @return the value of field 'MarkUnlinked'. + */ + public boolean isMarkUnlinked( + ) { + return this._markUnlinked; + } + + /** + * Returns the value of field 'showBootstrap'. + * + * @return the value of field 'ShowBootstrap'. + */ + public boolean isShowBootstrap( + ) { + return this._showBootstrap; + } + + /** + * Returns the value of field 'showDistances'. + * + * @return the value of field 'ShowDistances'. + */ + public boolean isShowDistances( + ) { + return this._showDistances; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'currentTree'. + * + * @param currentTree the value of field 'currentTree'. + */ + public void setCurrentTree( + final boolean currentTree) { + this._currentTree = currentTree; + this._has_currentTree = true; + } + + /** + * Sets the value of field 'fitToWindow'. + * + * @param fitToWindow the value of field 'fitToWindow'. + */ + public void setFitToWindow( + final boolean fitToWindow) { + this._fitToWindow = fitToWindow; + this._has_fitToWindow = true; + } + + /** + * Sets the value of field 'fontName'. + * + * @param fontName the value of field 'fontName'. + */ + public void setFontName( + final java.lang.String fontName) { + this._fontName = fontName; + } + + /** + * Sets the value of field 'fontSize'. + * + * @param fontSize the value of field 'fontSize'. + */ + public void setFontSize( + final int fontSize) { + this._fontSize = fontSize; + this._has_fontSize = true; + } + + /** + * Sets the value of field 'fontStyle'. + * + * @param fontStyle the value of field 'fontStyle'. + */ + public void setFontStyle( + final int fontStyle) { + this._fontStyle = fontStyle; + this._has_fontStyle = true; + } + + /** + * Sets the value of field 'height'. + * + * @param height the value of field 'height'. + */ + public void setHeight( + final int height) { + this._height = height; + this._has_height = true; + } + + /** + * Sets the value of field 'id'. The field 'id' has the + * following description: Tree ID added for binding tree + * visualization settings to vamsas document trees in jalview + * 2.4.1 + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'markUnlinked'. + * + * @param markUnlinked the value of field 'markUnlinked'. + */ + public void setMarkUnlinked( + final boolean markUnlinked) { + this._markUnlinked = markUnlinked; + this._has_markUnlinked = true; + } + + /** + * Sets the value of field 'newick'. + * + * @param newick the value of field 'newick'. + */ + public void setNewick( + final java.lang.String newick) { + this._newick = newick; + } + + /** + * Sets the value of field 'showBootstrap'. + * + * @param showBootstrap the value of field 'showBootstrap'. + */ + public void setShowBootstrap( + final boolean showBootstrap) { + this._showBootstrap = showBootstrap; + this._has_showBootstrap = true; + } + + /** + * Sets the value of field 'showDistances'. + * + * @param showDistances the value of field 'showDistances'. + */ + public void setShowDistances( + final boolean showDistances) { + this._showDistances = showDistances; + this._has_showDistances = true; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle( + final java.lang.String title) { + this._title = title; + } + + /** + * Sets the value of field 'width'. + * + * @param width the value of field 'width'. + */ + public void setWidth( + final int width) { + this._width = width; + this._has_width = true; + } + + /** + * Sets the value of field 'xpos'. + * + * @param xpos the value of field 'xpos'. + */ + public void setXpos( + final int xpos) { + this._xpos = xpos; + this._has_xpos = true; + } + + /** + * Sets the value of field 'ypos'. + * + * @param ypos the value of field 'ypos'. + */ + public void setYpos( + final int ypos) { + this._ypos = ypos; + this._has_ypos = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.Tree + */ + public static jalview.schemabinding.version2.Tree unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java index 3cb65e0..de531a8 100755 --- a/src/jalview/schemabinding/version2/UserColourScheme.java +++ b/src/jalview/schemabinding/version2/UserColourScheme.java @@ -1,117 +1,117 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 UserColourScheme. - * - * @version $Revision$ $Date$ - */ -public class UserColourScheme extends JalviewUserColours -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColourScheme() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 UserColourScheme. + * + * @version $Revision$ $Date$ + */ +public class UserColourScheme extends JalviewUserColours +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColourScheme() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.JalviewUserColours + */ + public static jalview.schemabinding.version2.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java index 062024f..8c56e0c 100755 --- a/src/jalview/schemabinding/version2/UserColours.java +++ b/src/jalview/schemabinding/version2/UserColours.java @@ -1,170 +1,170 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 UserColours. - * - * @version $Revision$ $Date$ - */ -public class UserColours implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _userColourScheme. - */ - private jalview.schemabinding.version2.UserColourScheme _userColourScheme; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColours() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'userColourScheme'. - * - * @return the value of field 'UserColourScheme'. - */ - public jalview.schemabinding.version2.UserColourScheme getUserColourScheme( - ) { - return this._userColourScheme; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme the value of field 'userColourScheme' - */ - public void setUserColourScheme( - final jalview.schemabinding.version2.UserColourScheme userColourScheme) { - this._userColourScheme = userColourScheme; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.UserColours - */ - public static jalview.schemabinding.version2.UserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 UserColours. + * + * @version $Revision$ $Date$ + */ +public class UserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _userColourScheme. + */ + private jalview.schemabinding.version2.UserColourScheme _userColourScheme; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColours() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'userColourScheme'. + * + * @return the value of field 'UserColourScheme'. + */ + public jalview.schemabinding.version2.UserColourScheme getUserColourScheme( + ) { + return this._userColourScheme; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'userColourScheme'. + * + * @param userColourScheme the value of field 'userColourScheme' + */ + public void setUserColourScheme( + final jalview.schemabinding.version2.UserColourScheme userColourScheme) { + this._userColourScheme = userColourScheme; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.UserColours + */ + public static jalview.schemabinding.version2.UserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index ae8e17f..8605dc5 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -1,429 +1,429 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList. - */ - private java.util.Vector _sequenceSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() { - super(); - this._treeList = new java.util.Vector(); - this._sequenceSetList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSet( - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetList.addElement(vSequenceSet); - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSet( - final int index, - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetList.add(index, vSequenceSet); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTree( - final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addTree( - final int index, - final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException { - this._treeList.add(index, vTree); - } - - /** - * Method enumerateSequenceSet. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SequenceSet elements - */ - public java.util.Enumeration enumerateSequenceSet( - ) { - return this._sequenceSetList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateTree( - ) { - return this._treeList.elements(); - } - - /** - * Method getSequenceSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.SequenceSet at the given index - */ - public jalview.schemabinding.version2.SequenceSet getSequenceSet( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index); - } - - /** - * Method getSequenceSet.Returns the contents of the collection - * in an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.SequenceSet[] getSequenceSet( - ) { - jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; - return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array); - } - - /** - * Method getSequenceSetCount. - * - * @return the size of this collection - */ - public int getSequenceSetCount( - ) { - return this._sequenceSetList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getTree( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (java.lang.String) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an - * Array.

Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getTree( - ) { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount( - ) { - return this._treeList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSequenceSet( - ) { - this._sequenceSetList.clear(); - } - - /** - */ - public void removeAllTree( - ) { - this._treeList.clear(); - } - - /** - * Method removeSequenceSet. - * - * @param vSequenceSet - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSet( - final jalview.schemabinding.version2.SequenceSet vSequenceSet) { - boolean removed = _sequenceSetList.remove(vSequenceSet); - return removed; - } - - /** - * Method removeSequenceSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt( - final int index) { - java.lang.Object obj = this._sequenceSetList.remove(index); - return (jalview.schemabinding.version2.SequenceSet) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree( - final java.lang.String vTree) { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeTreeAt( - final int index) { - java.lang.Object obj = this._treeList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSequenceSet( - final int index, - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) { - throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); - } - - this._sequenceSetList.set(index, vSequenceSet); - } - - /** - * - * - * @param vSequenceSetArray - */ - public void setSequenceSet( - final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) { - //-- copy array - _sequenceSetList.clear(); - - for (int i = 0; i < vSequenceSetArray.length; i++) { - this._sequenceSetList.add(vSequenceSetArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setTree( - final int index, - final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree( - final java.lang.String[] vTreeArray) { - //-- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 VAMSAS. + * + * @version $Revision$ $Date$ + */ +public class VAMSAS implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList. + */ + private java.util.Vector _sequenceSetList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSAS() { + super(); + this._treeList = new java.util.Vector(); + this._sequenceSetList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSet( + final jalview.schemabinding.version2.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.addElement(vSequenceSet); + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSet( + final int index, + final jalview.schemabinding.version2.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.add(index, vSequenceSet); + } + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.addElement(vTree); + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final int index, + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.add(index, vTree); + } + + /** + * Method enumerateSequenceSet. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.SequenceSet elements + */ + public java.util.Enumeration enumerateSequenceSet( + ) { + return this._sequenceSetList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method getSequenceSet. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.SequenceSet at the given index + */ + public jalview.schemabinding.version2.SequenceSet getSequenceSet( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) { + throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index); + } + + /** + * Method getSequenceSet.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.SequenceSet[] getSequenceSet( + ) { + jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; + return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array); + } + + /** + * Method getSequenceSetCount. + * + * @return the size of this collection + */ + public int getSequenceSetCount( + ) { + return this._sequenceSetList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the java.lang.String at the given index + */ + public java.lang.String getTree( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (java.lang.String) _treeList.get(index); + } + + /** + * Method getTree.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public java.lang.String[] getTree( + ) { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount( + ) { + return this._treeList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllSequenceSet( + ) { + this._sequenceSetList.clear(); + } + + /** + */ + public void removeAllTree( + ) { + this._treeList.clear(); + } + + /** + * Method removeSequenceSet. + * + * @param vSequenceSet + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSet( + final jalview.schemabinding.version2.SequenceSet vSequenceSet) { + boolean removed = _sequenceSetList.remove(vSequenceSet); + return removed; + } + + /** + * Method removeSequenceSetAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt( + final int index) { + java.lang.Object obj = this._sequenceSetList.remove(index); + return (jalview.schemabinding.version2.SequenceSet) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree( + final java.lang.String vTree) { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeTreeAt( + final int index) { + java.lang.Object obj = this._treeList.remove(index); + return (java.lang.String) obj; + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSet( + final int index, + final jalview.schemabinding.version2.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) { + throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); + } + + this._sequenceSetList.set(index, vSequenceSet); + } + + /** + * + * + * @param vSequenceSetArray + */ + public void setSequenceSet( + final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) { + //-- copy array + _sequenceSetList.clear(); + + for (int i = 0; i < vSequenceSetArray.length; i++) { + this._sequenceSetList.add(vSequenceSetArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setTree( + final int index, + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree( + final java.lang.String[] vTreeArray) { + //-- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) { + this._treeList.add(vTreeArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.VAMSAS + */ + public static jalview.schemabinding.version2.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java index 26814dc..245bd3d 100755 --- a/src/jalview/schemabinding/version2/VamsasModel.java +++ b/src/jalview/schemabinding/version2/VamsasModel.java @@ -1,116 +1,116 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 VamsasModel. - * - * @version $Revision$ $Date$ - */ -public class VamsasModel extends VAMSAS -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasModel() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 VamsasModel. + * + * @version $Revision$ $Date$ + */ +public class VamsasModel extends VAMSAS +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VamsasModel() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.schemabinding.version2.VAMSAS + */ + public static jalview.schemabinding.version2.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 49b0db2..9d554e6 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,2434 +1,2434 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 Viewport. - * - * @version $Revision$ $Date$ - */ -public class Viewport implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _conservationSelected. - */ - private boolean _conservationSelected; - - /** - * keeps track of state for field: _conservationSelected - */ - private boolean _has_conservationSelected; - - /** - * Field _pidSelected. - */ - private boolean _pidSelected; - - /** - * keeps track of state for field: _pidSelected - */ - private boolean _has_pidSelected; - - /** - * Field _bgColour. - */ - private java.lang.String _bgColour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _showFullId. - */ - private boolean _showFullId; - - /** - * keeps track of state for field: _showFullId - */ - private boolean _has_showFullId; - - /** - * Field _rightAlignIds. - */ - private boolean _rightAlignIds; - - /** - * keeps track of state for field: _rightAlignIds - */ - private boolean _has_rightAlignIds; - - /** - * Field _showText. - */ - private boolean _showText; - - /** - * keeps track of state for field: _showText - */ - private boolean _has_showText; - - /** - * Field _showColourText. - */ - private boolean _showColourText; - - /** - * keeps track of state for field: _showColourText - */ - private boolean _has_showColourText; - - /** - * Field _showUnconserved. - */ - private boolean _showUnconserved = false; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * Field _showBoxes. - */ - private boolean _showBoxes; - - /** - * keeps track of state for field: _showBoxes - */ - private boolean _has_showBoxes; - - /** - * Field _wrapAlignment. - */ - private boolean _wrapAlignment; - - /** - * keeps track of state for field: _wrapAlignment - */ - private boolean _has_wrapAlignment; - - /** - * Field _renderGaps. - */ - private boolean _renderGaps; - - /** - * keeps track of state for field: _renderGaps - */ - private boolean _has_renderGaps; - - /** - * Field _showSequenceFeatures. - */ - private boolean _showSequenceFeatures; - - /** - * keeps track of state for field: _showSequenceFeatures - */ - private boolean _has_showSequenceFeatures; - - /** - * Field _showNPfeatureTooltip. - */ - private boolean _showNPfeatureTooltip; - - /** - * keeps track of state for field: _showNPfeatureTooltip - */ - private boolean _has_showNPfeatureTooltip; - - /** - * Field _showDbRefTooltip. - */ - private boolean _showDbRefTooltip; - - /** - * keeps track of state for field: _showDbRefTooltip - */ - private boolean _has_showDbRefTooltip; - - /** - * Field _followHighlight. - */ - private boolean _followHighlight = true; - - /** - * keeps track of state for field: _followHighlight - */ - private boolean _has_followHighlight; - - /** - * Field _followSelection. - */ - private boolean _followSelection = true; - - /** - * keeps track of state for field: _followSelection - */ - private boolean _has_followSelection; - - /** - * Field _showAnnotation. - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _centreColumnLabels. - */ - private boolean _centreColumnLabels = false; - - /** - * keeps track of state for field: _centreColumnLabels - */ - private boolean _has_centreColumnLabels; - - /** - * Field _showGroupConservation. - */ - private boolean _showGroupConservation = false; - - /** - * keeps track of state for field: _showGroupConservation - */ - private boolean _has_showGroupConservation; - - /** - * Field _showGroupConsensus. - */ - private boolean _showGroupConsensus = false; - - /** - * keeps track of state for field: _showGroupConsensus - */ - private boolean _has_showGroupConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _startRes. - */ - private int _startRes; - - /** - * keeps track of state for field: _startRes - */ - private boolean _has_startRes; - - /** - * Field _startSeq. - */ - private int _startSeq; - - /** - * keeps track of state for field: _startSeq - */ - private boolean _has_startSeq; - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _viewName. - */ - private java.lang.String _viewName; - - /** - * Field _sequenceSetId. - */ - private java.lang.String _sequenceSetId; - - /** - * Field _gatheredViews. - */ - private boolean _gatheredViews; - - /** - * keeps track of state for field: _gatheredViews - */ - private boolean _has_gatheredViews; - - /** - * Field _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * unique id used by jalview to synchronize between stored and - * instantiated views - * - */ - private java.lang.String _id; - - /** - * Field _annotationColours. - */ - private jalview.schemabinding.version2.AnnotationColours _annotationColours; - - /** - * Field _hiddenColumnsList. - */ - private java.util.Vector _hiddenColumnsList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Viewport() { - super(); - this._hiddenColumnsList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException { - this._hiddenColumnsList.addElement(vHiddenColumns); - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addHiddenColumns( - final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException { - this._hiddenColumnsList.add(index, vHiddenColumns); - } - - /** - */ - public void deleteCentreColumnLabels( - ) { - this._has_centreColumnLabels= false; - } - - /** - */ - public void deleteConsThreshold( - ) { - this._has_consThreshold= false; - } - - /** - */ - public void deleteConservationSelected( - ) { - this._has_conservationSelected= false; - } - - /** - */ - public void deleteFollowHighlight( - ) { - this._has_followHighlight= false; - } - - /** - */ - public void deleteFollowSelection( - ) { - this._has_followSelection= false; - } - - /** - */ - public void deleteFontSize( - ) { - this._has_fontSize= false; - } - - /** - */ - public void deleteFontStyle( - ) { - this._has_fontStyle= false; - } - - /** - */ - public void deleteGatheredViews( - ) { - this._has_gatheredViews= false; - } - - /** - */ - public void deleteHeight( - ) { - this._has_height= false; - } - - /** - */ - public void deleteIgnoreGapsinConsensus( - ) { - this._has_ignoreGapsinConsensus= false; - } - - /** - */ - public void deletePidSelected( - ) { - this._has_pidSelected= false; - } - - /** - */ - public void deletePidThreshold( - ) { - this._has_pidThreshold= false; - } - - /** - */ - public void deleteRenderGaps( - ) { - this._has_renderGaps= false; - } - - /** - */ - public void deleteRightAlignIds( - ) { - this._has_rightAlignIds= false; - } - - /** - */ - public void deleteShowAnnotation( - ) { - this._has_showAnnotation= false; - } - - /** - */ - public void deleteShowBoxes( - ) { - this._has_showBoxes= false; - } - - /** - */ - public void deleteShowColourText( - ) { - this._has_showColourText= false; - } - - /** - */ - public void deleteShowConsensusHistogram( - ) { - this._has_showConsensusHistogram= false; - } - - /** - */ - public void deleteShowDbRefTooltip( - ) { - this._has_showDbRefTooltip= false; - } - - /** - */ - public void deleteShowFullId( - ) { - this._has_showFullId= false; - } - - /** - */ - public void deleteShowGroupConsensus( - ) { - this._has_showGroupConsensus= false; - } - - /** - */ - public void deleteShowGroupConservation( - ) { - this._has_showGroupConservation= false; - } - - /** - */ - public void deleteShowNPfeatureTooltip( - ) { - this._has_showNPfeatureTooltip= false; - } - - /** - */ - public void deleteShowSequenceFeatures( - ) { - this._has_showSequenceFeatures= false; - } - - /** - */ - public void deleteShowSequenceLogo( - ) { - this._has_showSequenceLogo= false; - } - - /** - */ - public void deleteShowText( - ) { - this._has_showText= false; - } - - /** - */ - public void deleteShowUnconserved( - ) { - this._has_showUnconserved= false; - } - - /** - */ - public void deleteStartRes( - ) { - this._has_startRes= false; - } - - /** - */ - public void deleteStartSeq( - ) { - this._has_startSeq= false; - } - - /** - */ - public void deleteTextCol1( - ) { - this._has_textCol1= false; - } - - /** - */ - public void deleteTextCol2( - ) { - this._has_textCol2= false; - } - - /** - */ - public void deleteTextColThreshold( - ) { - this._has_textColThreshold= false; - } - - /** - */ - public void deleteWidth( - ) { - this._has_width= false; - } - - /** - */ - public void deleteWrapAlignment( - ) { - this._has_wrapAlignment= false; - } - - /** - */ - public void deleteXpos( - ) { - this._has_xpos= false; - } - - /** - */ - public void deleteYpos( - ) { - this._has_ypos= false; - } - - /** - * Method enumerateHiddenColumns. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.HiddenColumns elements - */ - public java.util.Enumeration enumerateHiddenColumns( - ) { - return this._hiddenColumnsList.elements(); - } - - /** - * Returns the value of field 'annotationColours'. - * - * @return the value of field 'AnnotationColours'. - */ - public jalview.schemabinding.version2.AnnotationColours getAnnotationColours( - ) { - return this._annotationColours; - } - - /** - * Returns the value of field 'bgColour'. - * - * @return the value of field 'BgColour'. - */ - public java.lang.String getBgColour( - ) { - return this._bgColour; - } - - /** - * Returns the value of field 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean getCentreColumnLabels( - ) { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold( - ) { - return this._consThreshold; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean getConservationSelected( - ) { - return this._conservationSelected; - } - - /** - * Returns the value of field 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean getFollowHighlight( - ) { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean getFollowSelection( - ) { - return this._followSelection; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName( - ) { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize( - ) { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle( - ) { - return this._fontStyle; - } - - /** - * Returns the value of field 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean getGatheredViews( - ) { - return this._gatheredViews; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight( - ) { - return this._height; - } - - /** - * Method getHiddenColumns. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.HiddenColumns at the given - * index - */ - public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) { - throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index); - } - - /** - * Method getHiddenColumns.Returns the contents of the - * collection in an Array.

Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns( - ) { - jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; - return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array); - } - - /** - * Method getHiddenColumnsCount. - * - * @return the size of this collection - */ - public int getHiddenColumnsCount( - ) { - return this._hiddenColumnsList.size(); - } - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: unique id used by jalview to - * synchronize between stored and instantiated views - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus( - ) { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean getPidSelected( - ) { - return this._pidSelected; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold( - ) { - return this._pidThreshold; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean getRenderGaps( - ) { - return this._renderGaps; - } - - /** - * Returns the value of field 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean getRightAlignIds( - ) { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'sequenceSetId'. - * - * @return the value of field 'SequenceSetId'. - */ - public java.lang.String getSequenceSetId( - ) { - return this._sequenceSetId; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean getShowAnnotation( - ) { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean getShowBoxes( - ) { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean getShowColourText( - ) { - return this._showColourText; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram( - ) { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean getShowDbRefTooltip( - ) { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean getShowFullId( - ) { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean getShowGroupConsensus( - ) { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean getShowGroupConservation( - ) { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean getShowNPfeatureTooltip( - ) { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean getShowSequenceFeatures( - ) { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo( - ) { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean getShowText( - ) { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved( - ) { - return this._showUnconserved; - } - - /** - * Returns the value of field 'startRes'. - * - * @return the value of field 'StartRes'. - */ - public int getStartRes( - ) { - return this._startRes; - } - - /** - * Returns the value of field 'startSeq'. - * - * @return the value of field 'StartSeq'. - */ - public int getStartSeq( - ) { - return this._startSeq; - } - - /** - * Returns the value of field 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1( - ) { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2( - ) { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold( - ) { - return this._textColThreshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle( - ) { - return this._title; - } - - /** - * Returns the value of field 'viewName'. - * - * @return the value of field 'ViewName'. - */ - public java.lang.String getViewName( - ) { - return this._viewName; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth( - ) { - return this._width; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean getWrapAlignment( - ) { - return this._wrapAlignment; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos( - ) { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos( - ) { - return this._ypos; - } - - /** - * Method hasCentreColumnLabels. - * - * @return true if at least one CentreColumnLabels has been adde - */ - public boolean hasCentreColumnLabels( - ) { - return this._has_centreColumnLabels; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold( - ) { - return this._has_consThreshold; - } - - /** - * Method hasConservationSelected. - * - * @return true if at least one ConservationSelected has been - * added - */ - public boolean hasConservationSelected( - ) { - return this._has_conservationSelected; - } - - /** - * Method hasFollowHighlight. - * - * @return true if at least one FollowHighlight has been added - */ - public boolean hasFollowHighlight( - ) { - return this._has_followHighlight; - } - - /** - * Method hasFollowSelection. - * - * @return true if at least one FollowSelection has been added - */ - public boolean hasFollowSelection( - ) { - return this._has_followSelection; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize( - ) { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle( - ) { - return this._has_fontStyle; - } - - /** - * Method hasGatheredViews. - * - * @return true if at least one GatheredViews has been added - */ - public boolean hasGatheredViews( - ) { - return this._has_gatheredViews; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight( - ) { - return this._has_height; - } - - /** - * Method hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been - * added - */ - public boolean hasIgnoreGapsinConsensus( - ) { - return this._has_ignoreGapsinConsensus; - } - - /** - * Method hasPidSelected. - * - * @return true if at least one PidSelected has been added - */ - public boolean hasPidSelected( - ) { - return this._has_pidSelected; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold( - ) { - return this._has_pidThreshold; - } - - /** - * Method hasRenderGaps. - * - * @return true if at least one RenderGaps has been added - */ - public boolean hasRenderGaps( - ) { - return this._has_renderGaps; - } - - /** - * Method hasRightAlignIds. - * - * @return true if at least one RightAlignIds has been added - */ - public boolean hasRightAlignIds( - ) { - return this._has_rightAlignIds; - } - - /** - * Method hasShowAnnotation. - * - * @return true if at least one ShowAnnotation has been added - */ - public boolean hasShowAnnotation( - ) { - return this._has_showAnnotation; - } - - /** - * Method hasShowBoxes. - * - * @return true if at least one ShowBoxes has been added - */ - public boolean hasShowBoxes( - ) { - return this._has_showBoxes; - } - - /** - * Method hasShowColourText. - * - * @return true if at least one ShowColourText has been added - */ - public boolean hasShowColourText( - ) { - return this._has_showColourText; - } - - /** - * Method hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been - * added - */ - public boolean hasShowConsensusHistogram( - ) { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowDbRefTooltip. - * - * @return true if at least one ShowDbRefTooltip has been added - */ - public boolean hasShowDbRefTooltip( - ) { - return this._has_showDbRefTooltip; - } - - /** - * Method hasShowFullId. - * - * @return true if at least one ShowFullId has been added - */ - public boolean hasShowFullId( - ) { - return this._has_showFullId; - } - - /** - * Method hasShowGroupConsensus. - * - * @return true if at least one ShowGroupConsensus has been adde - */ - public boolean hasShowGroupConsensus( - ) { - return this._has_showGroupConsensus; - } - - /** - * Method hasShowGroupConservation. - * - * @return true if at least one ShowGroupConservation has been - * added - */ - public boolean hasShowGroupConservation( - ) { - return this._has_showGroupConservation; - } - - /** - * Method hasShowNPfeatureTooltip. - * - * @return true if at least one ShowNPfeatureTooltip has been - * added - */ - public boolean hasShowNPfeatureTooltip( - ) { - return this._has_showNPfeatureTooltip; - } - - /** - * Method hasShowSequenceFeatures. - * - * @return true if at least one ShowSequenceFeatures has been - * added - */ - public boolean hasShowSequenceFeatures( - ) { - return this._has_showSequenceFeatures; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo( - ) { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowText. - * - * @return true if at least one ShowText has been added - */ - public boolean hasShowText( - ) { - return this._has_showText; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved( - ) { - return this._has_showUnconserved; - } - - /** - * Method hasStartRes. - * - * @return true if at least one StartRes has been added - */ - public boolean hasStartRes( - ) { - return this._has_startRes; - } - - /** - * Method hasStartSeq. - * - * @return true if at least one StartSeq has been added - */ - public boolean hasStartSeq( - ) { - return this._has_startSeq; - } - - /** - * Method hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1( - ) { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2( - ) { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold( - ) { - return this._has_textColThreshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth( - ) { - return this._has_width; - } - - /** - * Method hasWrapAlignment. - * - * @return true if at least one WrapAlignment has been added - */ - public boolean hasWrapAlignment( - ) { - return this._has_wrapAlignment; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos( - ) { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos( - ) { - return this._has_ypos; - } - - /** - * Returns the value of field 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean isCentreColumnLabels( - ) { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean isConservationSelected( - ) { - return this._conservationSelected; - } - - /** - * Returns the value of field 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean isFollowHighlight( - ) { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean isFollowSelection( - ) { - return this._followSelection; - } - - /** - * Returns the value of field 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean isGatheredViews( - ) { - return this._gatheredViews; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus( - ) { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean isPidSelected( - ) { - return this._pidSelected; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean isRenderGaps( - ) { - return this._renderGaps; - } - - /** - * Returns the value of field 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean isRightAlignIds( - ) { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean isShowAnnotation( - ) { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean isShowBoxes( - ) { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean isShowColourText( - ) { - return this._showColourText; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram( - ) { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean isShowDbRefTooltip( - ) { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean isShowFullId( - ) { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean isShowGroupConsensus( - ) { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean isShowGroupConservation( - ) { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean isShowNPfeatureTooltip( - ) { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean isShowSequenceFeatures( - ) { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo( - ) { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean isShowText( - ) { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved( - ) { - return this._showUnconserved; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean isWrapAlignment( - ) { - return this._wrapAlignment; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllHiddenColumns( - ) { - this._hiddenColumnsList.clear(); - } - - /** - * Method removeHiddenColumns. - * - * @param vHiddenColumns - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) { - boolean removed = _hiddenColumnsList.remove(vHiddenColumns); - return removed; - } - - /** - * Method removeHiddenColumnsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( - final int index) { - java.lang.Object obj = this._hiddenColumnsList.remove(index); - return (jalview.schemabinding.version2.HiddenColumns) obj; - } - - /** - * Sets the value of field 'annotationColours'. - * - * @param annotationColours the value of field - * 'annotationColours'. - */ - public void setAnnotationColours( - final jalview.schemabinding.version2.AnnotationColours annotationColours) { - this._annotationColours = annotationColours; - } - - /** - * Sets the value of field 'bgColour'. - * - * @param bgColour the value of field 'bgColour'. - */ - public void setBgColour( - final java.lang.String bgColour) { - this._bgColour = bgColour; - } - - /** - * Sets the value of field 'centreColumnLabels'. - * - * @param centreColumnLabels the value of field - * 'centreColumnLabels'. - */ - public void setCentreColumnLabels( - final boolean centreColumnLabels) { - this._centreColumnLabels = centreColumnLabels; - this._has_centreColumnLabels = true; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold the value of field 'consThreshold'. - */ - public void setConsThreshold( - final int consThreshold) { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'conservationSelected'. - * - * @param conservationSelected the value of field - * 'conservationSelected'. - */ - public void setConservationSelected( - final boolean conservationSelected) { - this._conservationSelected = conservationSelected; - this._has_conservationSelected = true; - } - - /** - * Sets the value of field 'followHighlight'. - * - * @param followHighlight the value of field 'followHighlight'. - */ - public void setFollowHighlight( - final boolean followHighlight) { - this._followHighlight = followHighlight; - this._has_followHighlight = true; - } - - /** - * Sets the value of field 'followSelection'. - * - * @param followSelection the value of field 'followSelection'. - */ - public void setFollowSelection( - final boolean followSelection) { - this._followSelection = followSelection; - this._has_followSelection = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName the value of field 'fontName'. - */ - public void setFontName( - final java.lang.String fontName) { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize the value of field 'fontSize'. - */ - public void setFontSize( - final int fontSize) { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle the value of field 'fontStyle'. - */ - public void setFontStyle( - final int fontStyle) { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'gatheredViews'. - * - * @param gatheredViews the value of field 'gatheredViews'. - */ - public void setGatheredViews( - final boolean gatheredViews) { - this._gatheredViews = gatheredViews; - this._has_gatheredViews = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height the value of field 'height'. - */ - public void setHeight( - final int height) { - this._height = height; - this._has_height = true; - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setHiddenColumns( - final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) { - throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); - } - - this._hiddenColumnsList.set(index, vHiddenColumns); - } - - /** - * - * - * @param vHiddenColumnsArray - */ - public void setHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) { - //-- copy array - _hiddenColumnsList.clear(); - - for (int i = 0; i < vHiddenColumnsArray.length; i++) { - this._hiddenColumnsList.add(vHiddenColumnsArray[i]); - } - } - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: unique id used by jalview to - * synchronize between stored and instantiated views - * - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus the value of field - * 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus( - final boolean ignoreGapsinConsensus) { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = true; - } - - /** - * Sets the value of field 'pidSelected'. - * - * @param pidSelected the value of field 'pidSelected'. - */ - public void setPidSelected( - final boolean pidSelected) { - this._pidSelected = pidSelected; - this._has_pidSelected = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold the value of field 'pidThreshold'. - */ - public void setPidThreshold( - final int pidThreshold) { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * Sets the value of field 'renderGaps'. - * - * @param renderGaps the value of field 'renderGaps'. - */ - public void setRenderGaps( - final boolean renderGaps) { - this._renderGaps = renderGaps; - this._has_renderGaps = true; - } - - /** - * Sets the value of field 'rightAlignIds'. - * - * @param rightAlignIds the value of field 'rightAlignIds'. - */ - public void setRightAlignIds( - final boolean rightAlignIds) { - this._rightAlignIds = rightAlignIds; - this._has_rightAlignIds = true; - } - - /** - * Sets the value of field 'sequenceSetId'. - * - * @param sequenceSetId the value of field 'sequenceSetId'. - */ - public void setSequenceSetId( - final java.lang.String sequenceSetId) { - this._sequenceSetId = sequenceSetId; - } - - /** - * Sets the value of field 'showAnnotation'. - * - * @param showAnnotation the value of field 'showAnnotation'. - */ - public void setShowAnnotation( - final boolean showAnnotation) { - this._showAnnotation = showAnnotation; - this._has_showAnnotation = true; - } - - /** - * Sets the value of field 'showBoxes'. - * - * @param showBoxes the value of field 'showBoxes'. - */ - public void setShowBoxes( - final boolean showBoxes) { - this._showBoxes = showBoxes; - this._has_showBoxes = true; - } - - /** - * Sets the value of field 'showColourText'. - * - * @param showColourText the value of field 'showColourText'. - */ - public void setShowColourText( - final boolean showColourText) { - this._showColourText = showColourText; - this._has_showColourText = true; - } - - /** - * Sets the value of field 'showConsensusHistogram'. - * - * @param showConsensusHistogram the value of field - * 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram( - final boolean showConsensusHistogram) { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showDbRefTooltip'. - * - * @param showDbRefTooltip the value of field 'showDbRefTooltip' - */ - public void setShowDbRefTooltip( - final boolean showDbRefTooltip) { - this._showDbRefTooltip = showDbRefTooltip; - this._has_showDbRefTooltip = true; - } - - /** - * Sets the value of field 'showFullId'. - * - * @param showFullId the value of field 'showFullId'. - */ - public void setShowFullId( - final boolean showFullId) { - this._showFullId = showFullId; - this._has_showFullId = true; - } - - /** - * Sets the value of field 'showGroupConsensus'. - * - * @param showGroupConsensus the value of field - * 'showGroupConsensus'. - */ - public void setShowGroupConsensus( - final boolean showGroupConsensus) { - this._showGroupConsensus = showGroupConsensus; - this._has_showGroupConsensus = true; - } - - /** - * Sets the value of field 'showGroupConservation'. - * - * @param showGroupConservation the value of field - * 'showGroupConservation'. - */ - public void setShowGroupConservation( - final boolean showGroupConservation) { - this._showGroupConservation = showGroupConservation; - this._has_showGroupConservation = true; - } - - /** - * Sets the value of field 'showNPfeatureTooltip'. - * - * @param showNPfeatureTooltip the value of field - * 'showNPfeatureTooltip'. - */ - public void setShowNPfeatureTooltip( - final boolean showNPfeatureTooltip) { - this._showNPfeatureTooltip = showNPfeatureTooltip; - this._has_showNPfeatureTooltip = true; - } - - /** - * Sets the value of field 'showSequenceFeatures'. - * - * @param showSequenceFeatures the value of field - * 'showSequenceFeatures'. - */ - public void setShowSequenceFeatures( - final boolean showSequenceFeatures) { - this._showSequenceFeatures = showSequenceFeatures; - this._has_showSequenceFeatures = true; - } - - /** - * Sets the value of field 'showSequenceLogo'. - * - * @param showSequenceLogo the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo( - final boolean showSequenceLogo) { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = true; - } - - /** - * Sets the value of field 'showText'. - * - * @param showText the value of field 'showText'. - */ - public void setShowText( - final boolean showText) { - this._showText = showText; - this._has_showText = true; - } - - /** - * Sets the value of field 'showUnconserved'. - * - * @param showUnconserved the value of field 'showUnconserved'. - */ - public void setShowUnconserved( - final boolean showUnconserved) { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = true; - } - - /** - * Sets the value of field 'startRes'. - * - * @param startRes the value of field 'startRes'. - */ - public void setStartRes( - final int startRes) { - this._startRes = startRes; - this._has_startRes = true; - } - - /** - * Sets the value of field 'startSeq'. - * - * @param startSeq the value of field 'startSeq'. - */ - public void setStartSeq( - final int startSeq) { - this._startSeq = startSeq; - this._has_startSeq = true; - } - - /** - * Sets the value of field 'textCol1'. - * - * @param textCol1 the value of field 'textCol1'. - */ - public void setTextCol1( - final int textCol1) { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 the value of field 'textCol2'. - */ - public void setTextCol2( - final int textCol2) { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold the value of field 'textColThreshold' - */ - public void setTextColThreshold( - final int textColThreshold) { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle( - final java.lang.String title) { - this._title = title; - } - - /** - * Sets the value of field 'viewName'. - * - * @param viewName the value of field 'viewName'. - */ - public void setViewName( - final java.lang.String viewName) { - this._viewName = viewName; - } - - /** - * Sets the value of field 'width'. - * - * @param width the value of field 'width'. - */ - public void setWidth( - final int width) { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'wrapAlignment'. - * - * @param wrapAlignment the value of field 'wrapAlignment'. - */ - public void setWrapAlignment( - final boolean wrapAlignment) { - this._wrapAlignment = wrapAlignment; - this._has_wrapAlignment = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos the value of field 'xpos'. - */ - public void setXpos( - final int xpos) { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos the value of field 'ypos'. - */ - public void setYpos( - final int ypos) { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.Viewport - */ - public static jalview.schemabinding.version2.Viewport unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 Viewport. + * + * @version $Revision$ $Date$ + */ +public class Viewport implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _conservationSelected. + */ + private boolean _conservationSelected; + + /** + * keeps track of state for field: _conservationSelected + */ + private boolean _has_conservationSelected; + + /** + * Field _pidSelected. + */ + private boolean _pidSelected; + + /** + * keeps track of state for field: _pidSelected + */ + private boolean _has_pidSelected; + + /** + * Field _bgColour. + */ + private java.lang.String _bgColour; + + /** + * Field _consThreshold. + */ + private int _consThreshold; + + /** + * keeps track of state for field: _consThreshold + */ + private boolean _has_consThreshold; + + /** + * Field _pidThreshold. + */ + private int _pidThreshold; + + /** + * keeps track of state for field: _pidThreshold + */ + private boolean _has_pidThreshold; + + /** + * Field _title. + */ + private java.lang.String _title; + + /** + * Field _showFullId. + */ + private boolean _showFullId; + + /** + * keeps track of state for field: _showFullId + */ + private boolean _has_showFullId; + + /** + * Field _rightAlignIds. + */ + private boolean _rightAlignIds; + + /** + * keeps track of state for field: _rightAlignIds + */ + private boolean _has_rightAlignIds; + + /** + * Field _showText. + */ + private boolean _showText; + + /** + * keeps track of state for field: _showText + */ + private boolean _has_showText; + + /** + * Field _showColourText. + */ + private boolean _showColourText; + + /** + * keeps track of state for field: _showColourText + */ + private boolean _has_showColourText; + + /** + * Field _showUnconserved. + */ + private boolean _showUnconserved = false; + + /** + * keeps track of state for field: _showUnconserved + */ + private boolean _has_showUnconserved; + + /** + * Field _showBoxes. + */ + private boolean _showBoxes; + + /** + * keeps track of state for field: _showBoxes + */ + private boolean _has_showBoxes; + + /** + * Field _wrapAlignment. + */ + private boolean _wrapAlignment; + + /** + * keeps track of state for field: _wrapAlignment + */ + private boolean _has_wrapAlignment; + + /** + * Field _renderGaps. + */ + private boolean _renderGaps; + + /** + * keeps track of state for field: _renderGaps + */ + private boolean _has_renderGaps; + + /** + * Field _showSequenceFeatures. + */ + private boolean _showSequenceFeatures; + + /** + * keeps track of state for field: _showSequenceFeatures + */ + private boolean _has_showSequenceFeatures; + + /** + * Field _showNPfeatureTooltip. + */ + private boolean _showNPfeatureTooltip; + + /** + * keeps track of state for field: _showNPfeatureTooltip + */ + private boolean _has_showNPfeatureTooltip; + + /** + * Field _showDbRefTooltip. + */ + private boolean _showDbRefTooltip; + + /** + * keeps track of state for field: _showDbRefTooltip + */ + private boolean _has_showDbRefTooltip; + + /** + * Field _followHighlight. + */ + private boolean _followHighlight = true; + + /** + * keeps track of state for field: _followHighlight + */ + private boolean _has_followHighlight; + + /** + * Field _followSelection. + */ + private boolean _followSelection = true; + + /** + * keeps track of state for field: _followSelection + */ + private boolean _has_followSelection; + + /** + * Field _showAnnotation. + */ + private boolean _showAnnotation; + + /** + * keeps track of state for field: _showAnnotation + */ + private boolean _has_showAnnotation; + + /** + * Field _centreColumnLabels. + */ + private boolean _centreColumnLabels = false; + + /** + * keeps track of state for field: _centreColumnLabels + */ + private boolean _has_centreColumnLabels; + + /** + * Field _showGroupConservation. + */ + private boolean _showGroupConservation = false; + + /** + * keeps track of state for field: _showGroupConservation + */ + private boolean _has_showGroupConservation; + + /** + * Field _showGroupConsensus. + */ + private boolean _showGroupConsensus = false; + + /** + * keeps track of state for field: _showGroupConsensus + */ + private boolean _has_showGroupConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showSequenceLogo. + */ + private boolean _showSequenceLogo = false; + + /** + * keeps track of state for field: _showSequenceLogo + */ + private boolean _has_showSequenceLogo; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * Field _xpos. + */ + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos. + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; + + /** + * Field _width. + */ + private int _width; + + /** + * keeps track of state for field: _width + */ + private boolean _has_width; + + /** + * Field _height. + */ + private int _height; + + /** + * keeps track of state for field: _height + */ + private boolean _has_height; + + /** + * Field _startRes. + */ + private int _startRes; + + /** + * keeps track of state for field: _startRes + */ + private boolean _has_startRes; + + /** + * Field _startSeq. + */ + private int _startSeq; + + /** + * keeps track of state for field: _startSeq + */ + private boolean _has_startSeq; + + /** + * Field _fontName. + */ + private java.lang.String _fontName; + + /** + * Field _fontSize. + */ + private int _fontSize; + + /** + * keeps track of state for field: _fontSize + */ + private boolean _has_fontSize; + + /** + * Field _fontStyle. + */ + private int _fontStyle; + + /** + * keeps track of state for field: _fontStyle + */ + private boolean _has_fontStyle; + + /** + * Field _viewName. + */ + private java.lang.String _viewName; + + /** + * Field _sequenceSetId. + */ + private java.lang.String _sequenceSetId; + + /** + * Field _gatheredViews. + */ + private boolean _gatheredViews; + + /** + * keeps track of state for field: _gatheredViews + */ + private boolean _has_gatheredViews; + + /** + * Field _textCol1. + */ + private int _textCol1; + + /** + * keeps track of state for field: _textCol1 + */ + private boolean _has_textCol1; + + /** + * Field _textCol2. + */ + private int _textCol2; + + /** + * keeps track of state for field: _textCol2 + */ + private boolean _has_textCol2; + + /** + * Field _textColThreshold. + */ + private int _textColThreshold; + + /** + * keeps track of state for field: _textColThreshold + */ + private boolean _has_textColThreshold; + + /** + * unique id used by jalview to synchronize between stored and + * instantiated views + * + */ + private java.lang.String _id; + + /** + * Field _annotationColours. + */ + private jalview.schemabinding.version2.AnnotationColours _annotationColours; + + /** + * Field _hiddenColumnsList. + */ + private java.util.Vector _hiddenColumnsList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Viewport() { + super(); + this._hiddenColumnsList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + this._hiddenColumnsList.addElement(vHiddenColumns); + } + + /** + * + * + * @param index + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenColumns( + final int index, + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + this._hiddenColumnsList.add(index, vHiddenColumns); + } + + /** + */ + public void deleteCentreColumnLabels( + ) { + this._has_centreColumnLabels= false; + } + + /** + */ + public void deleteConsThreshold( + ) { + this._has_consThreshold= false; + } + + /** + */ + public void deleteConservationSelected( + ) { + this._has_conservationSelected= false; + } + + /** + */ + public void deleteFollowHighlight( + ) { + this._has_followHighlight= false; + } + + /** + */ + public void deleteFollowSelection( + ) { + this._has_followSelection= false; + } + + /** + */ + public void deleteFontSize( + ) { + this._has_fontSize= false; + } + + /** + */ + public void deleteFontStyle( + ) { + this._has_fontStyle= false; + } + + /** + */ + public void deleteGatheredViews( + ) { + this._has_gatheredViews= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ + public void deletePidSelected( + ) { + this._has_pidSelected= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteRenderGaps( + ) { + this._has_renderGaps= false; + } + + /** + */ + public void deleteRightAlignIds( + ) { + this._has_rightAlignIds= false; + } + + /** + */ + public void deleteShowAnnotation( + ) { + this._has_showAnnotation= false; + } + + /** + */ + public void deleteShowBoxes( + ) { + this._has_showBoxes= false; + } + + /** + */ + public void deleteShowColourText( + ) { + this._has_showColourText= false; + } + + /** + */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowDbRefTooltip( + ) { + this._has_showDbRefTooltip= false; + } + + /** + */ + public void deleteShowFullId( + ) { + this._has_showFullId= false; + } + + /** + */ + public void deleteShowGroupConsensus( + ) { + this._has_showGroupConsensus= false; + } + + /** + */ + public void deleteShowGroupConservation( + ) { + this._has_showGroupConservation= false; + } + + /** + */ + public void deleteShowNPfeatureTooltip( + ) { + this._has_showNPfeatureTooltip= false; + } + + /** + */ + public void deleteShowSequenceFeatures( + ) { + this._has_showSequenceFeatures= false; + } + + /** + */ + public void deleteShowSequenceLogo( + ) { + this._has_showSequenceLogo= false; + } + + /** + */ + public void deleteShowText( + ) { + this._has_showText= false; + } + + /** + */ + public void deleteShowUnconserved( + ) { + this._has_showUnconserved= false; + } + + /** + */ + public void deleteStartRes( + ) { + this._has_startRes= false; + } + + /** + */ + public void deleteStartSeq( + ) { + this._has_startSeq= false; + } + + /** + */ + public void deleteTextCol1( + ) { + this._has_textCol1= false; + } + + /** + */ + public void deleteTextCol2( + ) { + this._has_textCol2= false; + } + + /** + */ + public void deleteTextColThreshold( + ) { + this._has_textColThreshold= false; + } + + /** + */ + public void deleteWidth( + ) { + this._has_width= false; + } + + /** + */ + public void deleteWrapAlignment( + ) { + this._has_wrapAlignment= false; + } + + /** + */ + public void deleteXpos( + ) { + this._has_xpos= false; + } + + /** + */ + public void deleteYpos( + ) { + this._has_ypos= false; + } + + /** + * Method enumerateHiddenColumns. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.HiddenColumns elements + */ + public java.util.Enumeration enumerateHiddenColumns( + ) { + return this._hiddenColumnsList.elements(); + } + + /** + * Returns the value of field 'annotationColours'. + * + * @return the value of field 'AnnotationColours'. + */ + public jalview.schemabinding.version2.AnnotationColours getAnnotationColours( + ) { + return this._annotationColours; + } + + /** + * Returns the value of field 'bgColour'. + * + * @return the value of field 'BgColour'. + */ + public java.lang.String getBgColour( + ) { + return this._bgColour; + } + + /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean getCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** + * Returns the value of field 'consThreshold'. + * + * @return the value of field 'ConsThreshold'. + */ + public int getConsThreshold( + ) { + return this._consThreshold; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean getConservationSelected( + ) { + return this._conservationSelected; + } + + /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean getFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean getFollowSelection( + ) { + return this._followSelection; + } + + /** + * Returns the value of field 'fontName'. + * + * @return the value of field 'FontName'. + */ + public java.lang.String getFontName( + ) { + return this._fontName; + } + + /** + * Returns the value of field 'fontSize'. + * + * @return the value of field 'FontSize'. + */ + public int getFontSize( + ) { + return this._fontSize; + } + + /** + * Returns the value of field 'fontStyle'. + * + * @return the value of field 'FontStyle'. + */ + public int getFontStyle( + ) { + return this._fontStyle; + } + + /** + * Returns the value of field 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean getGatheredViews( + ) { + return this._gatheredViews; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Method getHiddenColumns. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.HiddenColumns at the given + * index + */ + public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenColumnsList.size()) { + throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index); + } + + /** + * Method getHiddenColumns.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns( + ) { + jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; + return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array); + } + + /** + * Method getHiddenColumnsCount. + * + * @return the size of this collection + */ + public int getHiddenColumnsCount( + ) { + return this._hiddenColumnsList.size(); + } + + /** + * Returns the value of field 'id'. The field 'id' has the + * following description: unique id used by jalview to + * synchronize between stored and instantiated views + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean getPidSelected( + ) { + return this._pidSelected; + } + + /** + * Returns the value of field 'pidThreshold'. + * + * @return the value of field 'PidThreshold'. + */ + public int getPidThreshold( + ) { + return this._pidThreshold; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean getRenderGaps( + ) { + return this._renderGaps; + } + + /** + * Returns the value of field 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean getRightAlignIds( + ) { + return this._rightAlignIds; + } + + /** + * Returns the value of field 'sequenceSetId'. + * + * @return the value of field 'SequenceSetId'. + */ + public java.lang.String getSequenceSetId( + ) { + return this._sequenceSetId; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean getShowAnnotation( + ) { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean getShowBoxes( + ) { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean getShowColourText( + ) { + return this._showColourText; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean getShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean getShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean getShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean getShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean getShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean getShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean getShowText( + ) { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * Returns the value of field 'startRes'. + * + * @return the value of field 'StartRes'. + */ + public int getStartRes( + ) { + return this._startRes; + } + + /** + * Returns the value of field 'startSeq'. + * + * @return the value of field 'StartSeq'. + */ + public int getStartSeq( + ) { + return this._startSeq; + } + + /** + * Returns the value of field 'textCol1'. + * + * @return the value of field 'TextCol1'. + */ + public int getTextCol1( + ) { + return this._textCol1; + } + + /** + * Returns the value of field 'textCol2'. + * + * @return the value of field 'TextCol2'. + */ + public int getTextCol2( + ) { + return this._textCol2; + } + + /** + * Returns the value of field 'textColThreshold'. + * + * @return the value of field 'TextColThreshold'. + */ + public int getTextColThreshold( + ) { + return this._textColThreshold; + } + + /** + * Returns the value of field 'title'. + * + * @return the value of field 'Title'. + */ + public java.lang.String getTitle( + ) { + return this._title; + } + + /** + * Returns the value of field 'viewName'. + * + * @return the value of field 'ViewName'. + */ + public java.lang.String getViewName( + ) { + return this._viewName; + } + + /** + * Returns the value of field 'width'. + * + * @return the value of field 'Width'. + */ + public int getWidth( + ) { + return this._width; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean getWrapAlignment( + ) { + return this._wrapAlignment; + } + + /** + * Returns the value of field 'xpos'. + * + * @return the value of field 'Xpos'. + */ + public int getXpos( + ) { + return this._xpos; + } + + /** + * Returns the value of field 'ypos'. + * + * @return the value of field 'Ypos'. + */ + public int getYpos( + ) { + return this._ypos; + } + + /** + * Method hasCentreColumnLabels. + * + * @return true if at least one CentreColumnLabels has been adde + */ + public boolean hasCentreColumnLabels( + ) { + return this._has_centreColumnLabels; + } + + /** + * Method hasConsThreshold. + * + * @return true if at least one ConsThreshold has been added + */ + public boolean hasConsThreshold( + ) { + return this._has_consThreshold; + } + + /** + * Method hasConservationSelected. + * + * @return true if at least one ConservationSelected has been + * added + */ + public boolean hasConservationSelected( + ) { + return this._has_conservationSelected; + } + + /** + * Method hasFollowHighlight. + * + * @return true if at least one FollowHighlight has been added + */ + public boolean hasFollowHighlight( + ) { + return this._has_followHighlight; + } + + /** + * Method hasFollowSelection. + * + * @return true if at least one FollowSelection has been added + */ + public boolean hasFollowSelection( + ) { + return this._has_followSelection; + } + + /** + * Method hasFontSize. + * + * @return true if at least one FontSize has been added + */ + public boolean hasFontSize( + ) { + return this._has_fontSize; + } + + /** + * Method hasFontStyle. + * + * @return true if at least one FontStyle has been added + */ + public boolean hasFontStyle( + ) { + return this._has_fontStyle; + } + + /** + * Method hasGatheredViews. + * + * @return true if at least one GatheredViews has been added + */ + public boolean hasGatheredViews( + ) { + return this._has_gatheredViews; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** + * Method hasPidSelected. + * + * @return true if at least one PidSelected has been added + */ + public boolean hasPidSelected( + ) { + return this._has_pidSelected; + } + + /** + * Method hasPidThreshold. + * + * @return true if at least one PidThreshold has been added + */ + public boolean hasPidThreshold( + ) { + return this._has_pidThreshold; + } + + /** + * Method hasRenderGaps. + * + * @return true if at least one RenderGaps has been added + */ + public boolean hasRenderGaps( + ) { + return this._has_renderGaps; + } + + /** + * Method hasRightAlignIds. + * + * @return true if at least one RightAlignIds has been added + */ + public boolean hasRightAlignIds( + ) { + return this._has_rightAlignIds; + } + + /** + * Method hasShowAnnotation. + * + * @return true if at least one ShowAnnotation has been added + */ + public boolean hasShowAnnotation( + ) { + return this._has_showAnnotation; + } + + /** + * Method hasShowBoxes. + * + * @return true if at least one ShowBoxes has been added + */ + public boolean hasShowBoxes( + ) { + return this._has_showBoxes; + } + + /** + * Method hasShowColourText. + * + * @return true if at least one ShowColourText has been added + */ + public boolean hasShowColourText( + ) { + return this._has_showColourText; + } + + /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowDbRefTooltip. + * + * @return true if at least one ShowDbRefTooltip has been added + */ + public boolean hasShowDbRefTooltip( + ) { + return this._has_showDbRefTooltip; + } + + /** + * Method hasShowFullId. + * + * @return true if at least one ShowFullId has been added + */ + public boolean hasShowFullId( + ) { + return this._has_showFullId; + } + + /** + * Method hasShowGroupConsensus. + * + * @return true if at least one ShowGroupConsensus has been adde + */ + public boolean hasShowGroupConsensus( + ) { + return this._has_showGroupConsensus; + } + + /** + * Method hasShowGroupConservation. + * + * @return true if at least one ShowGroupConservation has been + * added + */ + public boolean hasShowGroupConservation( + ) { + return this._has_showGroupConservation; + } + + /** + * Method hasShowNPfeatureTooltip. + * + * @return true if at least one ShowNPfeatureTooltip has been + * added + */ + public boolean hasShowNPfeatureTooltip( + ) { + return this._has_showNPfeatureTooltip; + } + + /** + * Method hasShowSequenceFeatures. + * + * @return true if at least one ShowSequenceFeatures has been + * added + */ + public boolean hasShowSequenceFeatures( + ) { + return this._has_showSequenceFeatures; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo( + ) { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowText. + * + * @return true if at least one ShowText has been added + */ + public boolean hasShowText( + ) { + return this._has_showText; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved( + ) { + return this._has_showUnconserved; + } + + /** + * Method hasStartRes. + * + * @return true if at least one StartRes has been added + */ + public boolean hasStartRes( + ) { + return this._has_startRes; + } + + /** + * Method hasStartSeq. + * + * @return true if at least one StartSeq has been added + */ + public boolean hasStartSeq( + ) { + return this._has_startSeq; + } + + /** + * Method hasTextCol1. + * + * @return true if at least one TextCol1 has been added + */ + public boolean hasTextCol1( + ) { + return this._has_textCol1; + } + + /** + * Method hasTextCol2. + * + * @return true if at least one TextCol2 has been added + */ + public boolean hasTextCol2( + ) { + return this._has_textCol2; + } + + /** + * Method hasTextColThreshold. + * + * @return true if at least one TextColThreshold has been added + */ + public boolean hasTextColThreshold( + ) { + return this._has_textColThreshold; + } + + /** + * Method hasWidth. + * + * @return true if at least one Width has been added + */ + public boolean hasWidth( + ) { + return this._has_width; + } + + /** + * Method hasWrapAlignment. + * + * @return true if at least one WrapAlignment has been added + */ + public boolean hasWrapAlignment( + ) { + return this._has_wrapAlignment; + } + + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added + */ + public boolean hasXpos( + ) { + return this._has_xpos; + } + + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added + */ + public boolean hasYpos( + ) { + return this._has_ypos; + } + + /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean isCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean isConservationSelected( + ) { + return this._conservationSelected; + } + + /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean isFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean isFollowSelection( + ) { + return this._followSelection; + } + + /** + * Returns the value of field 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean isGatheredViews( + ) { + return this._gatheredViews; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean isPidSelected( + ) { + return this._pidSelected; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean isRenderGaps( + ) { + return this._renderGaps; + } + + /** + * Returns the value of field 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean isRightAlignIds( + ) { + return this._rightAlignIds; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean isShowAnnotation( + ) { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean isShowBoxes( + ) { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean isShowColourText( + ) { + return this._showColourText; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean isShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean isShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean isShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean isShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean isShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean isShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean isShowText( + ) { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean isWrapAlignment( + ) { + return this._wrapAlignment; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllHiddenColumns( + ) { + this._hiddenColumnsList.clear(); + } + + /** + * Method removeHiddenColumns. + * + * @param vHiddenColumns + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) { + boolean removed = _hiddenColumnsList.remove(vHiddenColumns); + return removed; + } + + /** + * Method removeHiddenColumnsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( + final int index) { + java.lang.Object obj = this._hiddenColumnsList.remove(index); + return (jalview.schemabinding.version2.HiddenColumns) obj; + } + + /** + * Sets the value of field 'annotationColours'. + * + * @param annotationColours the value of field + * 'annotationColours'. + */ + public void setAnnotationColours( + final jalview.schemabinding.version2.AnnotationColours annotationColours) { + this._annotationColours = annotationColours; + } + + /** + * Sets the value of field 'bgColour'. + * + * @param bgColour the value of field 'bgColour'. + */ + public void setBgColour( + final java.lang.String bgColour) { + this._bgColour = bgColour; + } + + /** + * Sets the value of field 'centreColumnLabels'. + * + * @param centreColumnLabels the value of field + * 'centreColumnLabels'. + */ + public void setCentreColumnLabels( + final boolean centreColumnLabels) { + this._centreColumnLabels = centreColumnLabels; + this._has_centreColumnLabels = true; + } + + /** + * Sets the value of field 'consThreshold'. + * + * @param consThreshold the value of field 'consThreshold'. + */ + public void setConsThreshold( + final int consThreshold) { + this._consThreshold = consThreshold; + this._has_consThreshold = true; + } + + /** + * Sets the value of field 'conservationSelected'. + * + * @param conservationSelected the value of field + * 'conservationSelected'. + */ + public void setConservationSelected( + final boolean conservationSelected) { + this._conservationSelected = conservationSelected; + this._has_conservationSelected = true; + } + + /** + * Sets the value of field 'followHighlight'. + * + * @param followHighlight the value of field 'followHighlight'. + */ + public void setFollowHighlight( + final boolean followHighlight) { + this._followHighlight = followHighlight; + this._has_followHighlight = true; + } + + /** + * Sets the value of field 'followSelection'. + * + * @param followSelection the value of field 'followSelection'. + */ + public void setFollowSelection( + final boolean followSelection) { + this._followSelection = followSelection; + this._has_followSelection = true; + } + + /** + * Sets the value of field 'fontName'. + * + * @param fontName the value of field 'fontName'. + */ + public void setFontName( + final java.lang.String fontName) { + this._fontName = fontName; + } + + /** + * Sets the value of field 'fontSize'. + * + * @param fontSize the value of field 'fontSize'. + */ + public void setFontSize( + final int fontSize) { + this._fontSize = fontSize; + this._has_fontSize = true; + } + + /** + * Sets the value of field 'fontStyle'. + * + * @param fontStyle the value of field 'fontStyle'. + */ + public void setFontStyle( + final int fontStyle) { + this._fontStyle = fontStyle; + this._has_fontStyle = true; + } + + /** + * Sets the value of field 'gatheredViews'. + * + * @param gatheredViews the value of field 'gatheredViews'. + */ + public void setGatheredViews( + final boolean gatheredViews) { + this._gatheredViews = gatheredViews; + this._has_gatheredViews = true; + } + + /** + * Sets the value of field 'height'. + * + * @param height the value of field 'height'. + */ + public void setHeight( + final int height) { + this._height = height; + this._has_height = true; + } + + /** + * + * + * @param index + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setHiddenColumns( + final int index, + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenColumnsList.size()) { + throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); + } + + this._hiddenColumnsList.set(index, vHiddenColumns); + } + + /** + * + * + * @param vHiddenColumnsArray + */ + public void setHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) { + //-- copy array + _hiddenColumnsList.clear(); + + for (int i = 0; i < vHiddenColumnsArray.length; i++) { + this._hiddenColumnsList.add(vHiddenColumnsArray[i]); + } + } + + /** + * Sets the value of field 'id'. The field 'id' has the + * following description: unique id used by jalview to + * synchronize between stored and instantiated views + * + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** + * Sets the value of field 'pidSelected'. + * + * @param pidSelected the value of field 'pidSelected'. + */ + public void setPidSelected( + final boolean pidSelected) { + this._pidSelected = pidSelected; + this._has_pidSelected = true; + } + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold the value of field 'pidThreshold'. + */ + public void setPidThreshold( + final int pidThreshold) { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } + + /** + * Sets the value of field 'renderGaps'. + * + * @param renderGaps the value of field 'renderGaps'. + */ + public void setRenderGaps( + final boolean renderGaps) { + this._renderGaps = renderGaps; + this._has_renderGaps = true; + } + + /** + * Sets the value of field 'rightAlignIds'. + * + * @param rightAlignIds the value of field 'rightAlignIds'. + */ + public void setRightAlignIds( + final boolean rightAlignIds) { + this._rightAlignIds = rightAlignIds; + this._has_rightAlignIds = true; + } + + /** + * Sets the value of field 'sequenceSetId'. + * + * @param sequenceSetId the value of field 'sequenceSetId'. + */ + public void setSequenceSetId( + final java.lang.String sequenceSetId) { + this._sequenceSetId = sequenceSetId; + } + + /** + * Sets the value of field 'showAnnotation'. + * + * @param showAnnotation the value of field 'showAnnotation'. + */ + public void setShowAnnotation( + final boolean showAnnotation) { + this._showAnnotation = showAnnotation; + this._has_showAnnotation = true; + } + + /** + * Sets the value of field 'showBoxes'. + * + * @param showBoxes the value of field 'showBoxes'. + */ + public void setShowBoxes( + final boolean showBoxes) { + this._showBoxes = showBoxes; + this._has_showBoxes = true; + } + + /** + * Sets the value of field 'showColourText'. + * + * @param showColourText the value of field 'showColourText'. + */ + public void setShowColourText( + final boolean showColourText) { + this._showColourText = showColourText; + this._has_showColourText = true; + } + + /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showDbRefTooltip'. + * + * @param showDbRefTooltip the value of field 'showDbRefTooltip' + */ + public void setShowDbRefTooltip( + final boolean showDbRefTooltip) { + this._showDbRefTooltip = showDbRefTooltip; + this._has_showDbRefTooltip = true; + } + + /** + * Sets the value of field 'showFullId'. + * + * @param showFullId the value of field 'showFullId'. + */ + public void setShowFullId( + final boolean showFullId) { + this._showFullId = showFullId; + this._has_showFullId = true; + } + + /** + * Sets the value of field 'showGroupConsensus'. + * + * @param showGroupConsensus the value of field + * 'showGroupConsensus'. + */ + public void setShowGroupConsensus( + final boolean showGroupConsensus) { + this._showGroupConsensus = showGroupConsensus; + this._has_showGroupConsensus = true; + } + + /** + * Sets the value of field 'showGroupConservation'. + * + * @param showGroupConservation the value of field + * 'showGroupConservation'. + */ + public void setShowGroupConservation( + final boolean showGroupConservation) { + this._showGroupConservation = showGroupConservation; + this._has_showGroupConservation = true; + } + + /** + * Sets the value of field 'showNPfeatureTooltip'. + * + * @param showNPfeatureTooltip the value of field + * 'showNPfeatureTooltip'. + */ + public void setShowNPfeatureTooltip( + final boolean showNPfeatureTooltip) { + this._showNPfeatureTooltip = showNPfeatureTooltip; + this._has_showNPfeatureTooltip = true; + } + + /** + * Sets the value of field 'showSequenceFeatures'. + * + * @param showSequenceFeatures the value of field + * 'showSequenceFeatures'. + */ + public void setShowSequenceFeatures( + final boolean showSequenceFeatures) { + this._showSequenceFeatures = showSequenceFeatures; + this._has_showSequenceFeatures = true; + } + + /** + * Sets the value of field 'showSequenceLogo'. + * + * @param showSequenceLogo the value of field 'showSequenceLogo' + */ + public void setShowSequenceLogo( + final boolean showSequenceLogo) { + this._showSequenceLogo = showSequenceLogo; + this._has_showSequenceLogo = true; + } + + /** + * Sets the value of field 'showText'. + * + * @param showText the value of field 'showText'. + */ + public void setShowText( + final boolean showText) { + this._showText = showText; + this._has_showText = true; + } + + /** + * Sets the value of field 'showUnconserved'. + * + * @param showUnconserved the value of field 'showUnconserved'. + */ + public void setShowUnconserved( + final boolean showUnconserved) { + this._showUnconserved = showUnconserved; + this._has_showUnconserved = true; + } + + /** + * Sets the value of field 'startRes'. + * + * @param startRes the value of field 'startRes'. + */ + public void setStartRes( + final int startRes) { + this._startRes = startRes; + this._has_startRes = true; + } + + /** + * Sets the value of field 'startSeq'. + * + * @param startSeq the value of field 'startSeq'. + */ + public void setStartSeq( + final int startSeq) { + this._startSeq = startSeq; + this._has_startSeq = true; + } + + /** + * Sets the value of field 'textCol1'. + * + * @param textCol1 the value of field 'textCol1'. + */ + public void setTextCol1( + final int textCol1) { + this._textCol1 = textCol1; + this._has_textCol1 = true; + } + + /** + * Sets the value of field 'textCol2'. + * + * @param textCol2 the value of field 'textCol2'. + */ + public void setTextCol2( + final int textCol2) { + this._textCol2 = textCol2; + this._has_textCol2 = true; + } + + /** + * Sets the value of field 'textColThreshold'. + * + * @param textColThreshold the value of field 'textColThreshold' + */ + public void setTextColThreshold( + final int textColThreshold) { + this._textColThreshold = textColThreshold; + this._has_textColThreshold = true; + } + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle( + final java.lang.String title) { + this._title = title; + } + + /** + * Sets the value of field 'viewName'. + * + * @param viewName the value of field 'viewName'. + */ + public void setViewName( + final java.lang.String viewName) { + this._viewName = viewName; + } + + /** + * Sets the value of field 'width'. + * + * @param width the value of field 'width'. + */ + public void setWidth( + final int width) { + this._width = width; + this._has_width = true; + } + + /** + * Sets the value of field 'wrapAlignment'. + * + * @param wrapAlignment the value of field 'wrapAlignment'. + */ + public void setWrapAlignment( + final boolean wrapAlignment) { + this._wrapAlignment = wrapAlignment; + this._has_wrapAlignment = true; + } + + /** + * Sets the value of field 'xpos'. + * + * @param xpos the value of field 'xpos'. + */ + public void setXpos( + final int xpos) { + this._xpos = xpos; + this._has_xpos = true; + } + + /** + * Sets the value of field 'ypos'. + * + * @param ypos the value of field 'ypos'. + */ + public void setYpos( + final int ypos) { + this._ypos = ypos; + this._has_ypos = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled + * jalview.schemabinding.version2.Viewport + */ + public static jalview.schemabinding.version2.Viewport unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java index fbc56a3..0d95592 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java @@ -1,234 +1,234 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AlcodMap; - -/** - * Class AlcodMapDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodMapDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodMap"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _dnasq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlcodMap target = (AlcodMap) object; - return target.getDnasq(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlcodMap target = (AlcodMap) object; - target.setDnasq( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dnasq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlcodMap target = (AlcodMap) object; - return target.getMapping(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlcodMap target = (AlcodMap) object; - target.setMapping( (jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.AlcodMap.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.AlcodMap; + +/** + * Class AlcodMapDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodMapDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "alcodMap"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _dnasq + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodMap target = (AlcodMap) object; + return target.getDnasq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodMap target = (AlcodMap) object; + target.setDnasq( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dnasq + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapping + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodMap target = (AlcodMap) object; + return target.getMapping(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodMap target = (AlcodMap) object; + target.setMapping( (jalview.schemabinding.version2.Mapping) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Mapping(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapping + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AlcodMap.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java index cd87309..c6be168 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java @@ -1,280 +1,280 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Alcodon; - -/** - * Class AlcodonDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodonDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodon"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _pos1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos1()) { return null; } - return new java.lang.Long(target.getPos1()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePos1(); - return; - } - target.setPos1( ((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pos1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _pos2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos2()) { return null; } - return new java.lang.Long(target.getPos2()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePos2(); - return; - } - target.setPos2( ((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pos2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _pos3 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos3()) { return null; } - return new java.lang.Long(target.getPos3()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePos3(); - return; - } - target.setPos3( ((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pos3 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Alcodon.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Alcodon; + +/** + * Class AlcodonDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodonDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "alcodon"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _pos1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos1()) { return null; } + return new java.lang.Long(target.getPos1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos1(); + return; + } + target.setPos1( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _pos2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos2()) { return null; } + return new java.lang.Long(target.getPos2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos2(); + return; + } + target.setPos2( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _pos3 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos3()) { return null; } + return new java.lang.Long(target.getPos3()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos3(); + return; + } + target.setPos3( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos3 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Alcodon.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java index 5341376..9d9551a 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java @@ -1,244 +1,244 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AlcodonFrame; - -/** - * Class AlcodonFrameDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodonFrameDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "AlcodonFrame"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _alcodonList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodon(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodon(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Alcodon(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alcodonList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alcodMapList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodMap(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodMap(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.AlcodMap(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alcodMapList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.AlcodonFrame.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.AlcodonFrame; + +/** + * Class AlcodonFrameDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodonFrameDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "AlcodonFrame"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _alcodonList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodonFrame target = (AlcodonFrame) object; + return target.getAlcodon(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.removeAllAlcodon(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Alcodon(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodonList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _alcodMapList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodonFrame target = (AlcodonFrame) object; + return target.getAlcodMap(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.removeAllAlcodMap(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AlcodMap(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodMapList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AlcodonFrame.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 3d32ff6..30f1dc9 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java @@ -1,403 +1,403 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AnnotationColours; - -/** - * Class AnnotationColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationColoursDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "AnnotationColours"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _aboveThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasAboveThreshold()) { return null; } - return new java.lang.Integer(target.getAboveThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAboveThreshold(); - return; - } - target.setAboveThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _aboveThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _annotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - return target.getAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - target.setAnnotation( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _annotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _minColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasMinColour()) { return null; } - return new java.lang.Integer(target.getMinColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMinColour(); - return; - } - target.setMinColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _minColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _maxColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasMaxColour()) { return null; } - return new java.lang.Integer(target.getMaxColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMaxColour(); - return; - } - target.setMaxColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _maxColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _colourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - return target.getColourScheme(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - target.setColourScheme( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasThreshold()) { return null; } - return new java.lang.Float(target.getThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteThreshold(); - return; - } - target.setThreshold( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.AnnotationColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.AnnotationColours; + +/** + * Class AnnotationColoursDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationColoursDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "AnnotationColours"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _aboveThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasAboveThreshold()) { return null; } + return new java.lang.Integer(target.getAboveThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAboveThreshold(); + return; + } + target.setAboveThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _aboveThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _annotation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + return target.getAnnotation(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + target.setAnnotation( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _annotation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _minColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasMinColour()) { return null; } + return new java.lang.Integer(target.getMinColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMinColour(); + return; + } + target.setMinColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _minColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _maxColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasMaxColour()) { return null; } + return new java.lang.Integer(target.getMaxColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMaxColour(); + return; + } + target.setMaxColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _maxColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _colourScheme + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + return target.getColourScheme(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + target.setColourScheme( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourScheme + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AnnotationColours.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java index c1910ee..4fc6887 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java @@ -1,883 +1,926 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Annotation; - -/** - * Class AnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Annotation"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraph()) { return null; } - return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setGraph( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _graphType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphType()) { return null; } - return new java.lang.Integer(target.getGraphType()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteGraphType(); - return; - } - target.setGraphType( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graphType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _sequenceRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getSequenceRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setSequenceRef( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _groupRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getGroupRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setGroupRef( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _groupRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _graphColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphColour()) { return null; } - return new java.lang.Integer(target.getGraphColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteGraphColour(); - return; - } - target.setGraphColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graphColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _graphGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphGroup()) { return null; } - return new java.lang.Integer(target.getGraphGroup()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteGraphGroup(); - return; - } - target.setGraphGroup( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graphGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _scoreOnly - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScoreOnly()) { return null; } - return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteScoreOnly(); - return; - } - target.setScoreOnly( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _scoreOnly - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScore()) { return null; } - return new java.lang.Double(target.getScore()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteScore(); - return; - } - target.setScore( ((java.lang.Double) value).doubleValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.DoubleValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DoubleValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-1.7976931348623157E308); - typeValidator.setMaxInclusive(1.7976931348623157E308); - } - desc.setValidator(fieldValidator); - //-- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasVisible()) { return null; } - return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteVisible(); - return; - } - target.setVisible( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _centreColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasCentreColLabels()) { return null; } - return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteCentreColLabels(); - return; - } - target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _centreColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _scaleColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScaleColLabels()) { return null; } - return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteScaleColLabels(); - return; - } - target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _scaleColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showAllColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasShowAllColLabels()) { return null; } - return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowAllColLabels(); - return; - } - target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showAllColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _autoCalculated - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasAutoCalculated()) { return null; } - return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAutoCalculated(); - return; - } - target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _autoCalculated - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getAnnotationElement(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Annotation target = (Annotation) object; - target.removeAllAnnotationElement(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getLabel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setLabel( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setDescription( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _thresholdLine - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getThresholdLine(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Annotation target = (Annotation) object; - target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.ThresholdLine(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _thresholdLine - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Annotation.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Annotation; + +/** + * Class AnnotationDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Annotation"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _graph + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraph()) { return null; } + return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setGraph( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graph + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _graphType + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphType()) { return null; } + return new java.lang.Integer(target.getGraphType()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphType(); + return; + } + target.setGraphType( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphType + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _sequenceRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getSequenceRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setSequenceRef( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _groupRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getGroupRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setGroupRef( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _groupRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _graphColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphColour()) { return null; } + return new java.lang.Integer(target.getGraphColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphColour(); + return; + } + target.setGraphColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _graphGroup + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphGroup()) { return null; } + return new java.lang.Integer(target.getGraphGroup()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphGroup(); + return; + } + target.setGraphGroup( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphGroup + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _graphHeight + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphHeight", "graphHeight", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphHeight()) { return null; } + return new java.lang.Integer(target.getGraphHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphHeight(); + return; + } + target.setGraphHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphHeight + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _scoreOnly + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScoreOnly()) { return null; } + return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScoreOnly(); + return; + } + target.setScoreOnly( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scoreOnly + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _score + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScore()) { return null; } + return new java.lang.Double(target.getScore()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScore(); + return; + } + target.setScore( ((java.lang.Double) value).doubleValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _score + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.DoubleValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.DoubleValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-1.7976931348623157E308); + typeValidator.setMaxInclusive(1.7976931348623157E308); + } + desc.setValidator(fieldValidator); + //-- _visible + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasVisible()) { return null; } + return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteVisible(); + return; + } + target.setVisible( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _visible + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _centreColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasCentreColLabels()) { return null; } + return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColLabels(); + return; + } + target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _scaleColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScaleColLabels()) { return null; } + return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScaleColLabels(); + return; + } + target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scaleColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showAllColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasShowAllColLabels()) { return null; } + return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowAllColLabels(); + return; + } + target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showAllColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _autoCalculated + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasAutoCalculated()) { return null; } + return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoCalculated(); + return; + } + target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoCalculated + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _annotationElementList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getAnnotationElement(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Annotation target = (Annotation) object; + target.removeAllAnnotationElement(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AnnotationElement(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationElementList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _label + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getLabel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setLabel( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _label + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _thresholdLine + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getThresholdLine(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.ThresholdLine(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _thresholdLine + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Annotation.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java index 61221a1..abc0041 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java @@ -1,405 +1,405 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AnnotationElement; - -/** - * Class AnnotationElementDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElementDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "annotationElement"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _position - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasPosition()) { return null; } - return new java.lang.Integer(target.getPosition()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setPosition( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _position - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasColour()) { return null; } - return new java.lang.Integer(target.getColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColour(); - return; - } - target.setColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _displayCharacter - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDisplayCharacter(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setDisplayCharacter( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _displayCharacter - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setDescription( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _secondaryStructure - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getSecondaryStructure(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setSecondaryStructure( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _secondaryStructure - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - typeValidator.setLength(1); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasValue()) { return null; } - return new java.lang.Float(target.getValue()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteValue(); - return; - } - target.setValue( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.AnnotationElement.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.AnnotationElement; + +/** + * Class AnnotationElementDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElementDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "annotationElement"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _position + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasPosition()) { return null; } + return new java.lang.Integer(target.getPosition()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setPosition( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _position + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _displayCharacter + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDisplayCharacter(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDisplayCharacter( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayCharacter + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _secondaryStructure + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getSecondaryStructure(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setSecondaryStructure( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _secondaryStructure + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + typeValidator.setLength(1); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasValue()) { return null; } + return new java.lang.Float(target.getValue()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteValue(); + return; + } + target.setValue( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AnnotationElement.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java index 40cc7a5..3f6ae2d 100644 --- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java @@ -1,517 +1,517 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Colour; - -/** - * Class ColourDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ColourDescriptor() { - super(); - _xmlName = "colour"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - target.setName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _RGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getRGB(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - target.setRGB( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _RGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _minRGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getMinRGB(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - target.setMinRGB( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _minRGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _threshType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getThreshType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - target.setThreshType( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasThreshold()) { return null; } - return new java.lang.Float(target.getThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteThreshold(); - return; - } - target.setThreshold( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMax()) { return null; } - return new java.lang.Float(target.getMax()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMax(); - return; - } - target.setMax( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMin()) { return null; } - return new java.lang.Float(target.getMin()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMin(); - return; - } - target.setMin( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasColourByLabel()) { return null; } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasAutoScale()) { return null; } - return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAutoScale(); - return; - } - target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Colour.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Colour; + +/** + * Class ColourDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ColourDescriptor() { + super(); + _xmlName = "colour"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _RGB + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getRGB(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setRGB( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _RGB + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _minRGB + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getMinRGB(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setMinRGB( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _minRGB + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _threshType + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getThreshType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setThreshType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshType + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _max + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasMax()) { return null; } + return new java.lang.Float(target.getMax()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMax(); + return; + } + target.setMax( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _max + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _min + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasMin()) { return null; } + return new java.lang.Float(target.getMin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMin(); + return; + } + target.setMin( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _min + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _colourByLabel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasColourByLabel()) { return null; } + return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourByLabel(); + return; + } + target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourByLabel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _autoScale + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasAutoScale()) { return null; } + return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoScale(); + return; + } + target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoScale + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Colour.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java index 1a55978..00f81d2 100644 --- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java @@ -1,304 +1,304 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.DBRef; - -/** - * Class DBRefDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DBRefDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "DBRef"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getSource(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DBRef target = (DBRef) object; - target.setSource( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _source - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DBRef target = (DBRef) object; - target.setVersion( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getAccessionId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DBRef target = (DBRef) object; - target.setAccessionId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _accessionId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getMapping(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DBRef target = (DBRef) object; - target.setMapping( (jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.DBRef.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.DBRef; + +/** + * Class DBRefDescriptor. + * + * @version $Revision$ $Date$ + */ +public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DBRefDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "DBRef"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _source + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getSource(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setSource( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _source + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _accessionId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getAccessionId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setAccessionId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _accessionId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapping + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getMapping(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setMapping( (jalview.schemabinding.version2.Mapping) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Mapping(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapping + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.DBRef.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java index 92c919e..019c680 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java @@ -1,481 +1,481 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Feature; - -/** - * Class FeatureDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeatureDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "feature"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _begin - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasBegin()) { return null; } - return new java.lang.Integer(target.getBegin()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setBegin( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _begin - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - target.setType( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - target.setDescription( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _status - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getStatus(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - target.setStatus( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _status - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _featureGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getFeatureGroup(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - target.setFeatureGroup( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _featureGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasScore()) { return null; } - return new java.lang.Float(target.getScore()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteScore(); - return; - } - target.setScore( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _otherDataList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getOtherData(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Feature target = (Feature) object; - target.addOtherData( (jalview.schemabinding.version2.OtherData) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Feature target = (Feature) object; - target.removeAllOtherData(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.OtherData(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _otherDataList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Feature.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Feature; + +/** + * Class FeatureDescriptor. + * + * @version $Revision$ $Date$ + */ +public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "feature"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _begin + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasBegin()) { return null; } + return new java.lang.Integer(target.getBegin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setBegin( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _begin + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _status + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getStatus(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setStatus( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _status + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _featureGroup + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getFeatureGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setFeatureGroup( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _featureGroup + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _score + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasScore()) { return null; } + return new java.lang.Float(target.getScore()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScore(); + return; + } + target.setScore( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _score + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _otherDataList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getOtherData(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.addOtherData( (jalview.schemabinding.version2.OtherData) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Feature target = (Feature) object; + target.removeAllOtherData(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.OtherData(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _otherDataList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Feature.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java index 930aac9..69ed769 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java @@ -1,244 +1,244 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.FeatureSettings; - -/** - * Class FeatureSettingsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeatureSettingsDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "FeatureSettings"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _settingList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getSetting(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - FeatureSettings target = (FeatureSettings) object; - target.addSetting( (jalview.schemabinding.version2.Setting) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - FeatureSettings target = (FeatureSettings) object; - target.removeAllSetting(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Setting(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _settingList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _groupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getGroup(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - FeatureSettings target = (FeatureSettings) object; - target.addGroup( (jalview.schemabinding.version2.Group) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - FeatureSettings target = (FeatureSettings) object; - target.removeAllGroup(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Group(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _groupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.FeatureSettings.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.FeatureSettings; + +/** + * Class FeatureSettingsDescriptor. + * + * @version $Revision$ $Date$ + */ +public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureSettingsDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "FeatureSettings"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _settingList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + FeatureSettings target = (FeatureSettings) object; + return target.getSetting(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + FeatureSettings target = (FeatureSettings) object; + target.addSetting( (jalview.schemabinding.version2.Setting) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + FeatureSettings target = (FeatureSettings) object; + target.removeAllSetting(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Setting(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _settingList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _groupList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + FeatureSettings target = (FeatureSettings) object; + return target.getGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + FeatureSettings target = (FeatureSettings) object; + target.addGroup( (jalview.schemabinding.version2.Group) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + FeatureSettings target = (FeatureSettings) object; + target.removeAllGroup(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Group(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _groupList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.FeatureSettings.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java index 380d46e..b292135 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java @@ -1,151 +1,151 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Features; - -/** - * Class FeaturesDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeaturesDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "features"; - _elementDefinition = true; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Features.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Features; + +/** + * Class FeaturesDescriptor. + * + * @version $Revision$ $Date$ + */ +public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeaturesDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "features"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Features.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java index 417dbbb..8c03e2e 100644 --- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java @@ -1,237 +1,237 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Group; - -/** - * Class GroupDescriptor. - * - * @version $Revision$ $Date$ - */ -public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public GroupDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "group"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Group target = (Group) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Group target = (Group) object; - target.setName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Group target = (Group) object; - if (!target.hasDisplay()) { return null; } - return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Group target = (Group) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setDisplay( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Group.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Group; + +/** + * Class GroupDescriptor. + * + * @version $Revision$ $Date$ + */ +public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public GroupDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "group"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Group target = (Group) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Group target = (Group) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _display + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Group target = (Group) object; + if (!target.hasDisplay()) { return null; } + return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Group target = (Group) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setDisplay( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _display + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Group.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java index f307ee4..9408f58 100644 --- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java @@ -1,243 +1,243 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.HiddenColumns; - -/** - * Class HiddenColumnsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public HiddenColumnsDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "hiddenColumns"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasStart()) { return null; } - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteStart(); - return; - } - target.setStart( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteEnd(); - return; - } - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.HiddenColumns.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.HiddenColumns; + +/** + * Class HiddenColumnsDescriptor. + * + * @version $Revision$ $Date$ + */ +public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public HiddenColumnsDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "hiddenColumns"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + HiddenColumns target = (HiddenColumns) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + HiddenColumns target = (HiddenColumns) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStart(); + return; + } + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + HiddenColumns target = (HiddenColumns) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + HiddenColumns target = (HiddenColumns) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteEnd(); + return; + } + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.HiddenColumns.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index 10965c3..bfc0b8f 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -1,950 +1,950 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JGroup; - -/** - * Class JGroupDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JGroupDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JGroup"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasStart()) { return null; } - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteStart(); - return; - } - target.setStart( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteEnd(); - return; - } - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - target.setName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getColour(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - target.setColour( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasConsThreshold()) { return null; } - return new java.lang.Integer(target.getConsThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasPidThreshold()) { return null; } - return new java.lang.Integer(target.getPidThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePidThreshold(); - return; - } - target.setPidThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _outlineColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasOutlineColour()) { return null; } - return new java.lang.Integer(target.getOutlineColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteOutlineColour(); - return; - } - target.setOutlineColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _outlineColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _displayBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayBoxes()) { return null; } - return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteDisplayBoxes(); - return; - } - target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _displayBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _displayText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayText()) { return null; } - return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteDisplayText(); - return; - } - target.setDisplayText( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _displayText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _colourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasColourText()) { return null; } - return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColourText(); - return; - } - target.setColourText( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol1()) { return null; } - return new java.lang.Integer(target.getTextCol1()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextCol1(); - return; - } - target.setTextCol1( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol2()) { return null; } - return new java.lang.Integer(target.getTextCol2()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextCol2(); - return; - } - target.setTextCol2( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextColThreshold()) { return null; } - return new java.lang.Integer(target.getTextColThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowUnconserved()) { return null; } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasIgnoreGapsinConsensus()) { return null; } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowConsensusHistogram()) { return null; } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowSequenceLogo()) { return null; } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _seqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getSeq(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JGroup target = (JGroup) object; - target.addSeq( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JGroup target = (JGroup) object; - target.removeAllSeq(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _seqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.JGroup.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.JGroup; + +/** + * Class JGroupDescriptor. + * + * @version $Revision$ $Date$ + */ +public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JGroupDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JGroup"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStart(); + return; + } + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteEnd(); + return; + } + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setColour( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _consThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasConsThreshold()) { return null; } + return new java.lang.Integer(target.getConsThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConsThreshold(); + return; + } + target.setConsThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _consThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _pidThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasPidThreshold()) { return null; } + return new java.lang.Integer(target.getPidThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidThreshold(); + return; + } + target.setPidThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _outlineColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasOutlineColour()) { return null; } + return new java.lang.Integer(target.getOutlineColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteOutlineColour(); + return; + } + target.setOutlineColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _outlineColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _displayBoxes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasDisplayBoxes()) { return null; } + return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteDisplayBoxes(); + return; + } + target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayBoxes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _displayText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasDisplayText()) { return null; } + return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteDisplayText(); + return; + } + target.setDisplayText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _colourText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasColourText()) { return null; } + return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourText(); + return; + } + target.setColourText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _textCol1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextCol1()) { return null; } + return new java.lang.Integer(target.getTextCol1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol1(); + return; + } + target.setTextCol1( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textCol2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextCol2()) { return null; } + return new java.lang.Integer(target.getTextCol2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol2(); + return; + } + target.setTextCol2( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textColThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextColThreshold()) { return null; } + return new java.lang.Integer(target.getTextColThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextColThreshold(); + return; + } + target.setTextColThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textColThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _showUnconserved + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowUnconserved()) { return null; } + return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowUnconserved(); + return; + } + target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showUnconserved + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceLogo + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowSequenceLogo()) { return null; } + return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceLogo(); + return; + } + target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceLogo + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _seqList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getSeq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.addSeq( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JGroup target = (JGroup) object; + target.removeAllSeq(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _seqList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JGroup.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java index 427702d..ab0eaaf 100644 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java @@ -1,503 +1,503 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JSeq; - -/** - * Class JSeqDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JSeqDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JSeq"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasColour()) { return null; } - return new java.lang.Integer(target.getColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColour(); - return; - } - target.setColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasStart()) { return null; } - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setStart( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _hidden - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasHidden()) { return null; } - return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteHidden(); - return; - } - target.setHidden( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _hidden - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _featuresList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getFeatures(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - target.addFeatures( (jalview.schemabinding.version2.Features) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JSeq target = (JSeq) object; - target.removeAllFeatures(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Features(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _featuresList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _pdbidsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getPdbids(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - target.addPdbids( (jalview.schemabinding.version2.Pdbids) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JSeq target = (JSeq) object; - target.removeAllPdbids(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Pdbids(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _pdbidsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _hiddenSequencesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getHiddenSequences(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.addHiddenSequences( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JSeq target = (JSeq) object; - target.removeAllHiddenSequences(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _hiddenSequencesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.JSeq.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.JSeq; + +/** + * Class JSeqDescriptor. + * + * @version $Revision$ $Date$ + */ +public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeqDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JSeq"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _hidden + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasHidden()) { return null; } + return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHidden(); + return; + } + target.setHidden( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _hidden + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _featuresList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getFeatures(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.addFeatures( (jalview.schemabinding.version2.Features) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllFeatures(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Features(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _featuresList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _pdbidsList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getPdbids(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.addPdbids( (jalview.schemabinding.version2.Pdbids) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllPdbids(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Pdbids(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _pdbidsList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _hiddenSequencesList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getHiddenSequences(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.addHiddenSequences( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllHiddenSequences(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _hiddenSequencesList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JSeq.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java index 9aad95c..be9c022 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java @@ -1,312 +1,312 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JalviewModel; - -/** - * Class JalviewModelDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JalviewModel"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _creationDate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getCreationDate(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModel target = (JalviewModel) object; - target.setCreationDate( (java.util.Date) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new java.util.Date(); - } - }; - handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _creationDate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.DateTimeValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModel target = (JalviewModel) object; - target.setVersion( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _vamsasModel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVamsasModel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModel target = (JalviewModel) object; - target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.VamsasModel(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _vamsasModel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _jalviewModelSequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getJalviewModelSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModel target = (JalviewModel) object; - target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.JalviewModelSequence(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor()); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _jalviewModelSequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.JalviewModel.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.JalviewModel; + +/** + * Class JalviewModelDescriptor. + * + * @version $Revision$ $Date$ + */ +public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JalviewModel"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _creationDate + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getCreationDate(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setCreationDate( (java.util.Date) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.util.Date(); + } + }; + handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler); + desc.setImmutable(true); + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _creationDate + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.DateTimeValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _vamsasModel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getVamsasModel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.VamsasModel(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _vamsasModel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _jalviewModelSequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getJalviewModelSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JalviewModelSequence(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor()); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _jalviewModelSequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewModel.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java index d6fd0ba..765cd8a 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java @@ -1,404 +1,404 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JalviewModelSequence; - -/** - * Class JalviewModelSequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelSequenceDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _JSeqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJSeq(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJSeq( (jalview.schemabinding.version2.JSeq) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJSeq(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.JSeq(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _JSeqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _JGroupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJGroup(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJGroup( (jalview.schemabinding.version2.JGroup) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJGroup(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.JGroup(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _JGroupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _viewportList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getViewport(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addViewport( (jalview.schemabinding.version2.Viewport) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllViewport(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Viewport(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _viewportList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _userColoursList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getUserColours(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addUserColours( (jalview.schemabinding.version2.UserColours) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllUserColours(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.UserColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _userColoursList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addTree( (jalview.schemabinding.version2.Tree) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _featureSettings - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getFeatureSettings(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewModelSequence target = (JalviewModelSequence) object; - target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.FeatureSettings(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _featureSettings - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.JalviewModelSequence.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.JalviewModelSequence; + +/** + * Class JalviewModelSequenceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequenceDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _JSeqList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getJSeq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addJSeq( (jalview.schemabinding.version2.JSeq) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllJSeq(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JSeq(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _JSeqList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _JGroupList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getJGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addJGroup( (jalview.schemabinding.version2.JGroup) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllJGroup(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JGroup(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _JGroupList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _viewportList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getViewport(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addViewport( (jalview.schemabinding.version2.Viewport) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllViewport(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Viewport(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _viewportList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _userColoursList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getUserColours(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addUserColours( (jalview.schemabinding.version2.UserColours) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllUserColours(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.UserColours(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _userColoursList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addTree( (jalview.schemabinding.version2.Tree) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllTree(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Tree(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _featureSettings + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getFeatureSettings(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.FeatureSettings(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _featureSettings + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewModelSequence.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java index d4b4d05..47d0769 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java @@ -1,276 +1,276 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Colour; -import jalview.schemabinding.version2.JalviewUserColours; - -/** - * Class JalviewUserColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewUserColoursDescriptor() { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "JalviewUserColours"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _schemeName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getSchemeName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewUserColours target = (JalviewUserColours) object; - target.setSchemeName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _schemeName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewUserColours target = (JalviewUserColours) object; - target.setVersion( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _colourList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getColour(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - JalviewUserColours target = (JalviewUserColours) object; - target.addColour( (Colour) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - JalviewUserColours target = (JalviewUserColours) object; - target.removeAllColour(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new Colour(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _colourList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.JalviewUserColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Colour; +import jalview.schemabinding.version2.JalviewUserColours; + +/** + * Class JalviewUserColoursDescriptor. + * + * @version $Revision$ $Date$ + */ +public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColoursDescriptor() { + super(); + _nsURI = "www.jalview.org/colours"; + _xmlName = "JalviewUserColours"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _schemeName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getSchemeName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.setSchemeName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _schemeName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _colourList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.addColour( (Colour) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.removeAllColour(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new Colour(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _colourList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewUserColours.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java index f39b18f..91dffbe 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java @@ -1,243 +1,243 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListFrom; - -/** - * Class MapListFromDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListFromDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListFrom"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasStart()) { return null; } - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setStart( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.MapListFrom.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.MapListFrom; + +/** + * Class MapListFromDescriptor. + * + * @version $Revision$ $Date$ + */ +public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListFromDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListFrom"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListFrom target = (MapListFrom) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListFrom target = (MapListFrom) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListFrom target = (MapListFrom) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListFrom target = (MapListFrom) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListFrom.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java index 4de1738..43a4033 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java @@ -1,243 +1,243 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListTo; - -/** - * Class MapListToDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListToDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListTo"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasStart()) { return null; } - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setStart( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasEnd()) { return null; } - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setEnd( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.MapListTo.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.MapListTo; + +/** + * Class MapListToDescriptor. + * + * @version $Revision$ $Date$ + */ +public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListToDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListTo"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListTo target = (MapListTo) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListTo target = (MapListTo) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListTo target = (MapListTo) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListTo target = (MapListTo) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListTo.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java index 7dc7bc5..8b92065 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java @@ -1,328 +1,328 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListType; - -/** - * Class MapListTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListTypeDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListType"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _mapFromUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapFromUnit()) { return null; } - return new java.lang.Long(target.getMapFromUnit()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setMapFromUnit( ((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mapFromUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); - } - desc.setValidator(fieldValidator); - //-- _mapToUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapToUnit()) { return null; } - return new java.lang.Long(target.getMapToUnit()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setMapToUnit( ((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mapToUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _mapListFromList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListFrom(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListType target = (MapListType) object; - target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - MapListType target = (MapListType) object; - target.removeAllMapListFrom(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.MapListFrom(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mapListFromList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _mapListToList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListTo(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapListType target = (MapListType) object; - target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - MapListType target = (MapListType) object; - target.removeAllMapListTo(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.MapListTo(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mapListToList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.MapListType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.MapListType; + +/** + * Class MapListTypeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListTypeDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListType"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _mapFromUnit + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + if (!target.hasMapFromUnit()) { return null; } + return new java.lang.Long(target.getMapFromUnit()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setMapFromUnit( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapFromUnit + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(1L); + } + desc.setValidator(fieldValidator); + //-- _mapToUnit + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + if (!target.hasMapToUnit()) { return null; } + return new java.lang.Long(target.getMapToUnit()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setMapToUnit( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapToUnit + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(1L); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapListFromList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + return target.getMapListFrom(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + MapListType target = (MapListType) object; + target.removeAllMapListFrom(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MapListFrom(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _mapListFromList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _mapListToList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + return target.getMapListTo(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + MapListType target = (MapListType) object; + target.removeAllMapListTo(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MapListTo(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _mapListToList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListType.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java index 63543d7..b0aa8f9 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java @@ -1,230 +1,230 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MappingChoice; - -/** - * Class MappingChoiceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MappingChoiceDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MappingChoice target = (MappingChoice) object; - target.setSequence( (jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dseqFor - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getDseqFor(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MappingChoice target = (MappingChoice) object; - target.setDseqFor( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dseqFor - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.MappingChoice.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.MappingChoice; + +/** + * Class MappingChoiceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingChoiceDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsChoice(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _sequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MappingChoice target = (MappingChoice) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MappingChoice target = (MappingChoice) object; + target.setSequence( (jalview.schemabinding.version2.Sequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _dseqFor + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MappingChoice target = (MappingChoice) object; + return target.getDseqFor(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MappingChoice target = (MappingChoice) object; + target.setDseqFor( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dseqFor + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MappingChoice.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java index 95e1a87..45157ff 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java @@ -1,196 +1,196 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Mapping; - -/** - * Class MappingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MappingDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Mapping"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _mappingChoice - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Mapping target = (Mapping) object; - return target.getMappingChoice(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Mapping target = (Mapping) object; - target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.MappingChoice(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor()); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mappingChoice - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Mapping.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Mapping; + +/** + * Class MappingDescriptor. + * + * @version $Revision$ $Date$ + */ +public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor()); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Mapping"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsChoice(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _mappingChoice + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Mapping target = (Mapping) object; + return target.getMappingChoice(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Mapping target = (Mapping) object; + target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MappingChoice(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor()); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mappingChoice + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Mapping.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java index 46f6682..201f4df 100644 --- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java @@ -1,235 +1,235 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.OtherData; - -/** - * Class OtherDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public OtherDataDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "otherData"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - OtherData target = (OtherData) object; - return target.getKey(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - OtherData target = (OtherData) object; - target.setKey( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - OtherData target = (OtherData) object; - return target.getValue(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - OtherData target = (OtherData) object; - target.setValue( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.OtherData.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.OtherData; + +/** + * Class OtherDataDescriptor. + * + * @version $Revision$ $Date$ + */ +public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public OtherDataDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "otherData"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _key + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + OtherData target = (OtherData) object; + return target.getKey(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + OtherData target = (OtherData) object; + target.setKey( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _key + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + OtherData target = (OtherData) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + OtherData target = (OtherData) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.OtherData.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java index dbf0c3a..548be45 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java @@ -1,312 +1,312 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Pdbentry; - -/** - * Class PdbentryDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbentryDescriptor() { - super(); - _xmlName = "pdbentry"; - _elementDefinition = false; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pdbentry target = (Pdbentry) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pdbentry target = (Pdbentry) object; - target.setType( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _file - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getFile(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pdbentry target = (Pdbentry) object; - target.setFile( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _file - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _items - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getPdbentryItem(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pdbentry target = (Pdbentry) object; - target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Pdbentry target = (Pdbentry) object; - target.removeAllPdbentryItem(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.PdbentryItem(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor()); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _items - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Pdbentry.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Pdbentry; + +/** + * Class PdbentryDescriptor. + * + * @version $Revision$ $Date$ + */ +public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryDescriptor() { + super(); + _xmlName = "pdbentry"; + _elementDefinition = false; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _file + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getFile(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setFile( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _file + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _items + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getPdbentryItem(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Pdbentry target = (Pdbentry) object; + target.removeAllPdbentryItem(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.PdbentryItem(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor()); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _items + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Pdbentry.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java index 693ad61..cb2b5da 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java @@ -1,202 +1,202 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.PdbentryItem; - -/** - * Class PdbentryItemDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbentryItemDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "pdbentry"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - PdbentryItem target = (PdbentryItem) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - PdbentryItem target = (PdbentryItem) object; - target.addProperty( (jalview.schemabinding.version2.Property) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - PdbentryItem target = (PdbentryItem) object; - target.removeAllProperty(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.PdbentryItem.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.PdbentryItem; + +/** + * Class PdbentryItemDescriptor. + * + * @version $Revision$ $Date$ + */ +public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryItemDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "pdbentry"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _propertyList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + PdbentryItem target = (PdbentryItem) object; + return target.getProperty(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + PdbentryItem target = (PdbentryItem) object; + target.addProperty( (jalview.schemabinding.version2.Property) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + PdbentryItem target = (PdbentryItem) object; + target.removeAllProperty(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Property(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _propertyList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.PdbentryItem.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java index 2547f1d..f005ce6 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java @@ -1,203 +1,203 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Pdbids; - -/** - * Class PdbidsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbidsDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "pdbids"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _structureStateList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pdbids target = (Pdbids) object; - return target.getStructureState(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pdbids target = (Pdbids) object; - target.addStructureState( (jalview.schemabinding.version2.StructureState) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Pdbids target = (Pdbids) object; - target.removeAllStructureState(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.StructureState(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _structureStateList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Pdbids.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Pdbids; + +/** + * Class PdbidsDescriptor. + * + * @version $Revision$ $Date$ + */ +public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbidsDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "pdbids"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _structureStateList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbids target = (Pdbids) object; + return target.getStructureState(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbids target = (Pdbids) object; + target.addStructureState( (jalview.schemabinding.version2.StructureState) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Pdbids target = (Pdbids) object; + target.removeAllStructureState(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.StructureState(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _structureStateList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Pdbids.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java index 15f2e37..b7087d2 100644 --- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java @@ -1,235 +1,235 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Property; - -/** - * Class PropertyDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PropertyDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "property"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Property target = (Property) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) object; - target.setName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Property target = (Property) object; - return target.getValue(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) object; - target.setValue( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Property.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Property; + +/** + * Class PropertyDescriptor. + * + * @version $Revision$ $Date$ + */ +public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PropertyDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "property"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Property target = (Property) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Property target = (Property) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Property target = (Property) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Property target = (Property) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Property.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java index 4dfd168..2de6b0a 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java @@ -1,240 +1,240 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Sequence; - -/** - * Class SequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Sequence"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _dsseqid - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDsseqid(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.setDsseqid( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dsseqid - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _DBRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDBRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.addDBRef( (jalview.schemabinding.version2.DBRef) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Sequence target = (Sequence) object; - target.removeAllDBRef(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.DBRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _DBRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Sequence.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Sequence; + +/** + * Class SequenceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor()); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Sequence"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _dsseqid + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDsseqid(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.setDsseqid( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dsseqid + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _DBRefList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDBRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.addDBRef( (jalview.schemabinding.version2.DBRef) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Sequence target = (Sequence) object; + target.removeAllDBRef(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.DBRef(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _DBRefList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Sequence.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java index aa0c798..1542223 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java @@ -1,404 +1,404 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceSet; - -/** - * Class SequenceSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSetDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceSet"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getGapChar(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setGapChar( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _datasetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getDatasetId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setDatasetId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _datasetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequence( (jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllSequence(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _annotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addAnnotation( (jalview.schemabinding.version2.Annotation) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllAnnotation(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Annotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _sequenceSetPropertiesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequenceSetProperties(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllSequenceSetProperties(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.SequenceSetProperties(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetPropertiesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alcodonFrameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAlcodonFrame(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllAlcodonFrame(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.AlcodonFrame(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alcodonFrameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.SequenceSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.SequenceSet; + +/** + * Class SequenceSetDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "SequenceSet"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _gapChar + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getGapChar(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setGapChar( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _gapChar + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _datasetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getDatasetId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setDatasetId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _datasetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequenceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequence( (jalview.schemabinding.version2.Sequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllSequence(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _annotationList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAnnotation(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addAnnotation( (jalview.schemabinding.version2.Annotation) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllAnnotation(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Annotation(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _sequenceSetPropertiesList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequenceSetProperties(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllSequenceSetProperties(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.SequenceSetProperties(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetPropertiesList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _alcodonFrameList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAlcodonFrame(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllAlcodonFrame(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AlcodonFrame(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodonFrameList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceSet.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java index 9c3c578..5c8be83 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java @@ -1,231 +1,231 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceSetProperties; - -/** - * Class SequenceSetPropertiesDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSetPropertiesDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "sequenceSetProperties"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getKey(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setKey( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getValue(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setValue( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.SequenceSetProperties.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.SequenceSetProperties; + +/** + * Class SequenceSetPropertiesDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetPropertiesDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "sequenceSetProperties"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _key + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetProperties target = (SequenceSetProperties) object; + return target.getKey(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetProperties target = (SequenceSetProperties) object; + target.setKey( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _key + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetProperties target = (SequenceSetProperties) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetProperties target = (SequenceSetProperties) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceSetProperties.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java index fa73621..27305e7 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java @@ -1,310 +1,310 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceType; - -/** - * Class SequenceTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceTypeDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceType"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setDescription( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setSequence( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.SequenceType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.SequenceType; + +/** + * Class SequenceTypeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceTypeDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "SequenceType"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setSequence( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceType.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java index 772e9bc..9c2de5b 100644 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java @@ -1,620 +1,620 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Setting; - -/** - * Class SettingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SettingDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "setting"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - target.setType( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColour()) { return null; } - return new java.lang.Integer(target.getColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasDisplay()) { return null; } - return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setDisplay( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _order - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasOrder()) { return null; } - return new java.lang.Float(target.getOrder()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteOrder(); - return; - } - target.setOrder( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _order - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _mincolour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMincolour()) { return null; } - return new java.lang.Integer(target.getMincolour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMincolour(); - return; - } - target.setMincolour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _mincolour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshold()) { return null; } - return new java.lang.Float(target.getThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteThreshold(); - return; - } - target.setThreshold( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _threshstate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshstate()) { return null; } - return new java.lang.Integer(target.getThreshstate()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteThreshstate(); - return; - } - target.setThreshstate( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshstate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMax()) { return null; } - return new java.lang.Float(target.getMax()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMax(); - return; - } - target.setMax( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMin()) { return null; } - return new java.lang.Float(target.getMin()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMin(); - return; - } - target.setMin( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColourByLabel()) { return null; } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasAutoScale()) { return null; } - return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAutoScale(); - return; - } - target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Setting.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Setting; + +/** + * Class SettingDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SettingDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "setting"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _display + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasDisplay()) { return null; } + return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setDisplay( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _display + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _order + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasOrder()) { return null; } + return new java.lang.Float(target.getOrder()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteOrder(); + return; + } + target.setOrder( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _order + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _mincolour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMincolour()) { return null; } + return new java.lang.Integer(target.getMincolour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMincolour(); + return; + } + target.setMincolour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mincolour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _threshstate + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasThreshstate()) { return null; } + return new java.lang.Integer(target.getThreshstate()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshstate(); + return; + } + target.setThreshstate( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshstate + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _max + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMax()) { return null; } + return new java.lang.Float(target.getMax()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMax(); + return; + } + target.setMax( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _max + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _min + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMin()) { return null; } + return new java.lang.Float(target.getMin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMin(); + return; + } + target.setMin( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _min + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _colourByLabel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasColourByLabel()) { return null; } + return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourByLabel(); + return; + } + target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourByLabel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _autoScale + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasAutoScale()) { return null; } + return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoScale(); + return; + } + target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoScale + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Setting.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java index fe61eb9..5330dfd 100644 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java @@ -1,525 +1,525 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.StructureState; - -/** - * Class StructureStateDescriptor. - * - * @version $Revision$ $Date$ - */ -public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public StructureStateDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "structureState"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - target.setContent( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasVisible()) { return null; } - return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteVisible(); - return; - } - target.setVisible( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasXpos()) { return null; } - return new java.lang.Integer(target.getXpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteXpos(); - return; - } - target.setXpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasYpos()) { return null; } - return new java.lang.Integer(target.getYpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteYpos(); - return; - } - target.setYpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasWidth()) { return null; } - return new java.lang.Integer(target.getWidth()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteWidth(); - return; - } - target.setWidth( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasHeight()) { return null; } - return new java.lang.Integer(target.getHeight()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteHeight(); - return; - } - target.setHeight( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _viewId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - return target.getViewId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - target.setViewId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _viewId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _alignwithAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasAlignwithAlignPanel()) { return null; } - return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAlignwithAlignPanel(); - return; - } - target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _alignwithAlignPanel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _colourwithAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasColourwithAlignPanel()) { return null; } - return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColourwithAlignPanel(); - return; - } - target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colourwithAlignPanel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.StructureState.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.StructureState; + +/** + * Class StructureStateDescriptor. + * + * @version $Revision$ $Date$ + */ +public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public StructureStateDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "structureState"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- _content + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + return target.getContent(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + target.setContent( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _content + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize attribute descriptors + + //-- _visible + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasVisible()) { return null; } + return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteVisible(); + return; + } + target.setVisible( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _visible + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _viewId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + return target.getViewId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + target.setViewId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _viewId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _alignwithAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasAlignwithAlignPanel()) { return null; } + return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAlignwithAlignPanel(); + return; + } + target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _alignwithAlignPanel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _colourwithAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasColourwithAlignPanel()) { return null; } + return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourwithAlignPanel(); + return; + } + target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourwithAlignPanel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.StructureState.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java index 951e7ca..851ccb2 100644 --- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java @@ -1,280 +1,280 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.ThresholdLine; - -/** - * Class ThresholdLineDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ThresholdLineDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "thresholdLine"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - return target.getLabel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ThresholdLine target = (ThresholdLine) object; - target.setLabel( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasValue()) { return null; } - return new java.lang.Float(target.getValue()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteValue(); - return; - } - target.setValue( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasColour()) { return null; } - return new java.lang.Integer(target.getColour()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteColour(); - return; - } - target.setColour( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.ThresholdLine.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.ThresholdLine; + +/** + * Class ThresholdLineDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ThresholdLineDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "thresholdLine"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _label + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + return target.getLabel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + target.setLabel( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _label + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + if (!target.hasValue()) { return null; } + return new java.lang.Float(target.getValue()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteValue(); + return; + } + target.setValue( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.ThresholdLine.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java index f4741a2..ed9952e 100644 --- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java @@ -1,815 +1,815 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Tree; - -/** - * Class TreeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public TreeDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "tree"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasWidth()) { return null; } - return new java.lang.Integer(target.getWidth()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteWidth(); - return; - } - target.setWidth( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasHeight()) { return null; } - return new java.lang.Integer(target.getHeight()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteHeight(); - return; - } - target.setHeight( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasXpos()) { return null; } - return new java.lang.Integer(target.getXpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteXpos(); - return; - } - target.setXpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasYpos()) { return null; } - return new java.lang.Integer(target.getYpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteYpos(); - return; - } - target.setYpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getFontName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setFontName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontSize()) { return null; } - return new java.lang.Integer(target.getFontSize()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFontSize(); - return; - } - target.setFontSize( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontStyle()) { return null; } - return new java.lang.Integer(target.getFontStyle()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFontStyle(); - return; - } - target.setFontStyle( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasThreshold()) { return null; } - return new java.lang.Float(target.getThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteThreshold(); - return; - } - target.setThreshold( ((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - //-- _showBootstrap - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowBootstrap()) { return null; } - return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowBootstrap(); - return; - } - target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showBootstrap - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showDistances - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowDistances()) { return null; } - return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowDistances(); - return; - } - target.setShowDistances( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showDistances - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _markUnlinked - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasMarkUnlinked()) { return null; } - return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteMarkUnlinked(); - return; - } - target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _markUnlinked - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _fitToWindow - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFitToWindow()) { return null; } - return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFitToWindow(); - return; - } - target.setFitToWindow( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fitToWindow - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _currentTree - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasCurrentTree()) { return null; } - return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteCurrentTree(); - return; - } - target.setCurrentTree( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _currentTree - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setTitle( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _newick - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewick(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setNewick( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _newick - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Tree.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Tree; + +/** + * Class TreeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public TreeDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "tree"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getFontName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setFontName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _fontSize + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFontSize()) { return null; } + return new java.lang.Integer(target.getFontSize()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontSize(); + return; + } + target.setFontSize( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontSize + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontStyle + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFontStyle()) { return null; } + return new java.lang.Integer(target.getFontStyle()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontStyle(); + return; + } + target.setFontStyle( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontStyle + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _showBootstrap + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasShowBootstrap()) { return null; } + return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowBootstrap(); + return; + } + target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showBootstrap + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showDistances + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasShowDistances()) { return null; } + return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowDistances(); + return; + } + target.setShowDistances( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showDistances + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _markUnlinked + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasMarkUnlinked()) { return null; } + return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMarkUnlinked(); + return; + } + target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _markUnlinked + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _fitToWindow + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFitToWindow()) { return null; } + return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFitToWindow(); + return; + } + target.setFitToWindow( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fitToWindow + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _currentTree + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasCurrentTree()) { return null; } + return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCurrentTree(); + return; + } + target.setCurrentTree( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _currentTree + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + super.setIdentity(desc); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IdValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IdValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getTitle(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setTitle( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _title + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _newick + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getNewick(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setNewick( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _newick + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Tree.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java index be7012a..7fcc16f 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java @@ -1,151 +1,151 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.UserColourScheme; - -/** - * Class UserColourSchemeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColourSchemeDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "UserColourScheme"; - _elementDefinition = true; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.UserColourScheme.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.UserColourScheme; + +/** + * Class UserColourSchemeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColourSchemeDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "UserColourScheme"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.UserColourScheme.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java index bda1c5e..e5e799b 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java @@ -1,232 +1,232 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.UserColours; - -/** - * Class UserColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColoursDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "UserColours"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - UserColours target = (UserColours) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - UserColours target = (UserColours) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _userColourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - UserColours target = (UserColours) object; - return target.getUserColourScheme(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - UserColours target = (UserColours) object; - target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.UserColourScheme(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _userColourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.UserColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.UserColours; + +/** + * Class UserColoursDescriptor. + * + * @version $Revision$ $Date$ + */ +public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColoursDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "UserColours"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + UserColours target = (UserColours) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + UserColours target = (UserColours) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _userColourScheme + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + UserColours target = (UserColours) object; + return target.getUserColourScheme(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + UserColours target = (UserColours) object; + target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.UserColourScheme(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _userColourScheme + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.UserColours.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java index 375f435..730fe2e 100644 --- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java @@ -1,249 +1,249 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.VAMSAS; - -/** - * Class VAMSASDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSASDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "VAMSAS"; - _elementDefinition = false; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addTree( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - VAMSAS target = (VAMSAS) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _sequenceSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getSequenceSet(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - VAMSAS target = (VAMSAS) object; - target.removeAllSequenceSet(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.SequenceSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.VAMSAS.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.VAMSAS; + +/** + * Class VAMSASDescriptor. + * + * @version $Revision$ $Date$ + */ +public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSASDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "VAMSAS"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addTree( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + VAMSAS target = (VAMSAS) object; + target.removeAllTree(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _sequenceSetList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getSequenceSet(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + VAMSAS target = (VAMSAS) object; + target.removeAllSequenceSet(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.SequenceSet(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.VAMSAS.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java index bc14cfd..584c096 100644 --- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java @@ -1,151 +1,151 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.VamsasModel; - -/** - * Class VamsasModelDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasModelDescriptor() { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "vamsasModel"; - _elementDefinition = true; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.VamsasModel.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.VamsasModel; + +/** + * Class VamsasModelDescriptor. + * + * @version $Revision$ $Date$ + */ +public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VamsasModelDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "vamsasModel"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.VamsasModel.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 21b8cf2..ed50a68 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1,1958 +1,1958 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Viewport; - -/** - * Class ViewportDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ViewportDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "Viewport"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _conservationSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConservationSelected()) { return null; } - return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteConservationSelected(); - return; - } - target.setConservationSelected( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _conservationSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _pidSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidSelected()) { return null; } - return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePidSelected(); - return; - } - target.setPidSelected( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pidSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _bgColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getBgColour(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setBgColour( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _bgColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConsThreshold()) { return null; } - return new java.lang.Integer(target.getConsThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidThreshold()) { return null; } - return new java.lang.Integer(target.getPidThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deletePidThreshold(); - return; - } - target.setPidThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setTitle( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _showFullId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowFullId()) { return null; } - return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowFullId(); - return; - } - target.setShowFullId( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showFullId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _rightAlignIds - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRightAlignIds()) { return null; } - return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteRightAlignIds(); - return; - } - target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _rightAlignIds - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowText()) { return null; } - return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowText(); - return; - } - target.setShowText( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showColourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowColourText()) { return null; } - return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowColourText(); - return; - } - target.setShowColourText( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showColourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowUnconserved()) { return null; } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowBoxes()) { return null; } - return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowBoxes(); - return; - } - target.setShowBoxes( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _wrapAlignment - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWrapAlignment()) { return null; } - return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteWrapAlignment(); - return; - } - target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _wrapAlignment - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _renderGaps - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRenderGaps()) { return null; } - return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteRenderGaps(); - return; - } - target.setRenderGaps( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _renderGaps - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showSequenceFeatures - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceFeatures()) { return null; } - return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowSequenceFeatures(); - return; - } - target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showSequenceFeatures - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showNPfeatureTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowNPfeatureTooltip()) { return null; } - return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowNPfeatureTooltip(); - return; - } - target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showNPfeatureTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showDbRefTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowDbRefTooltip()) { return null; } - return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowDbRefTooltip(); - return; - } - target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showDbRefTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _followHighlight - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowHighlight()) { return null; } - return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFollowHighlight(); - return; - } - target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _followHighlight - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _followSelection - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowSelection()) { return null; } - return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFollowSelection(); - return; - } - target.setFollowSelection( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _followSelection - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showAnnotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowAnnotation()) { return null; } - return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowAnnotation(); - return; - } - target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showAnnotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _centreColumnLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasCentreColumnLabels()) { return null; } - return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteCentreColumnLabels(); - return; - } - target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _centreColumnLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showGroupConservation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConservation()) { return null; } - return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowGroupConservation(); - return; - } - target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showGroupConservation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showGroupConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConsensus()) { return null; } - return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowGroupConsensus(); - return; - } - target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showGroupConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowConsensusHistogram()) { return null; } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceLogo()) { return null; } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasIgnoreGapsinConsensus()) { return null; } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasXpos()) { return null; } - return new java.lang.Integer(target.getXpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteXpos(); - return; - } - target.setXpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasYpos()) { return null; } - return new java.lang.Integer(target.getYpos()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteYpos(); - return; - } - target.setYpos( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWidth()) { return null; } - return new java.lang.Integer(target.getWidth()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteWidth(); - return; - } - target.setWidth( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasHeight()) { return null; } - return new java.lang.Integer(target.getHeight()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteHeight(); - return; - } - target.setHeight( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _startRes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartRes()) { return null; } - return new java.lang.Integer(target.getStartRes()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteStartRes(); - return; - } - target.setStartRes( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _startRes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _startSeq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartSeq()) { return null; } - return new java.lang.Integer(target.getStartSeq()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteStartSeq(); - return; - } - target.setStartSeq( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _startSeq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getFontName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setFontName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontSize()) { return null; } - return new java.lang.Integer(target.getFontSize()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFontSize(); - return; - } - target.setFontSize( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontStyle()) { return null; } - return new java.lang.Integer(target.getFontStyle()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFontStyle(); - return; - } - target.setFontStyle( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _viewName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getViewName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setViewName( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _viewName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _sequenceSetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getSequenceSetId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setSequenceSetId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _gatheredViews - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasGatheredViews()) { return null; } - return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteGatheredViews(); - return; - } - target.setGatheredViews( ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _gatheredViews - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol1()) { return null; } - return new java.lang.Integer(target.getTextCol1()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextCol1(); - return; - } - target.setTextCol1( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol2()) { return null; } - return new java.lang.Integer(target.getTextCol2()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextCol2(); - return; - } - target.setTextCol2( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextColThreshold()) { return null; } - return new java.lang.Integer(target.getTextColThreshold()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold( ((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setId( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _annotationColours - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getAnnotationColours(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.AnnotationColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _annotationColours - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _hiddenColumnsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getHiddenColumns(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Viewport target = (Viewport) object; - target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - Viewport target = (Viewport) object; - target.removeAllHiddenColumns(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.HiddenColumns(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _hiddenColumnsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.Viewport.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.Viewport; + +/** + * Class ViewportDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ViewportDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "Viewport"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _conservationSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConservationSelected()) { return null; } + return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConservationSelected(); + return; + } + target.setConservationSelected( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _conservationSelected + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _pidSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidSelected()) { return null; } + return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidSelected(); + return; + } + target.setPidSelected( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidSelected + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _bgColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getBgColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setBgColour( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _bgColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _consThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConsThreshold()) { return null; } + return new java.lang.Integer(target.getConsThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConsThreshold(); + return; + } + target.setConsThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _consThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _pidThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidThreshold()) { return null; } + return new java.lang.Integer(target.getPidThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidThreshold(); + return; + } + target.setPidThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getTitle(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setTitle( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _title + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _showFullId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowFullId()) { return null; } + return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowFullId(); + return; + } + target.setShowFullId( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showFullId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _rightAlignIds + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasRightAlignIds()) { return null; } + return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteRightAlignIds(); + return; + } + target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _rightAlignIds + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowText()) { return null; } + return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowText(); + return; + } + target.setShowText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showColourText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowColourText()) { return null; } + return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowColourText(); + return; + } + target.setShowColourText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showColourText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showUnconserved + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowUnconserved()) { return null; } + return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowUnconserved(); + return; + } + target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showUnconserved + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showBoxes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowBoxes()) { return null; } + return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowBoxes(); + return; + } + target.setShowBoxes( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showBoxes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _wrapAlignment + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasWrapAlignment()) { return null; } + return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWrapAlignment(); + return; + } + target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _wrapAlignment + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _renderGaps + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasRenderGaps()) { return null; } + return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteRenderGaps(); + return; + } + target.setRenderGaps( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _renderGaps + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceFeatures + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowSequenceFeatures()) { return null; } + return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceFeatures(); + return; + } + target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceFeatures + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showNPfeatureTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowNPfeatureTooltip()) { return null; } + return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowNPfeatureTooltip(); + return; + } + target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showNPfeatureTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showDbRefTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowDbRefTooltip()) { return null; } + return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowDbRefTooltip(); + return; + } + target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showDbRefTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followHighlight + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowHighlight()) { return null; } + return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowHighlight(); + return; + } + target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followHighlight + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followSelection + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowSelection()) { return null; } + return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowSelection(); + return; + } + target.setFollowSelection( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followSelection + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showAnnotation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowAnnotation()) { return null; } + return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowAnnotation(); + return; + } + target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showAnnotation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _centreColumnLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasCentreColumnLabels()) { return null; } + return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColumnLabels(); + return; + } + target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColumnLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConservation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConservation()) { return null; } + return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConservation(); + return; + } + target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConservation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConsensus()) { return null; } + return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConsensus(); + return; + } + target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceLogo + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowSequenceLogo()) { return null; } + return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceLogo(); + return; + } + target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceLogo + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _startRes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasStartRes()) { return null; } + return new java.lang.Integer(target.getStartRes()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStartRes(); + return; + } + target.setStartRes( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _startRes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _startSeq + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasStartSeq()) { return null; } + return new java.lang.Integer(target.getStartSeq()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStartSeq(); + return; + } + target.setStartSeq( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _startSeq + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getFontName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setFontName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _fontSize + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFontSize()) { return null; } + return new java.lang.Integer(target.getFontSize()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontSize(); + return; + } + target.setFontSize( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontSize + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontStyle + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFontStyle()) { return null; } + return new java.lang.Integer(target.getFontStyle()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontStyle(); + return; + } + target.setFontStyle( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontStyle + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _viewName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getViewName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setViewName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _viewName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _sequenceSetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getSequenceSetId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setSequenceSetId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _gatheredViews + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasGatheredViews()) { return null; } + return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGatheredViews(); + return; + } + target.setGatheredViews( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _gatheredViews + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _textCol1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextCol1()) { return null; } + return new java.lang.Integer(target.getTextCol1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol1(); + return; + } + target.setTextCol1( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textCol2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextCol2()) { return null; } + return new java.lang.Integer(target.getTextCol2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol2(); + return; + } + target.setTextCol2( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textColThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextColThreshold()) { return null; } + return new java.lang.Integer(target.getTextColThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextColThreshold(); + return; + } + target.setTextColThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textColThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + super.setIdentity(desc); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IdValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IdValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _annotationColours + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getAnnotationColours(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AnnotationColours(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _annotationColours + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _hiddenColumnsList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getHiddenColumns(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Viewport target = (Viewport) object; + target.removeAllHiddenColumns(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.HiddenColumns(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _hiddenColumnsList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Viewport.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } + +} -- 1.7.10.2