From: amwaterhouse Date: Tue, 1 Nov 2005 11:35:19 +0000 (+0000) Subject: New schema, new objects X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d801fe51c77f1555600b16655282ec87223392e9;p=jalview.git New schema, new objects --- diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java index 8143217..e3aa240 100755 --- a/src/org/vamsas/objects/core/Alignment.java +++ b/src/org/vamsas/objects/core/Alignment.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -80,8 +80,7 @@ public class Alignment implements java.io.Serializable { //- Constructors -/ //----------------/ - public Alignment() - { + public Alignment() { super(); _alignmentAnnotationsList = new Vector(); _treeList = new Vector(); @@ -243,7 +242,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentAnnotationsList.size())) { - throw new IndexOutOfBoundsException("getAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index); @@ -291,7 +290,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index); @@ -372,7 +371,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); @@ -561,7 +560,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentAnnotationsList.size())) { - throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index); } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations) @@ -595,7 +594,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _alignmentSequenceList.setElementAt(vAlignmentSequence, index); } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence) @@ -659,7 +658,7 @@ public class Alignment implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _treeList.setElementAt(vTree, index); } //-- void setTree(int, org.vamsas.objects.core.Tree) @@ -686,13 +685,13 @@ public class Alignment implements java.io.Serializable { * * * @param reader - * @return Alignment + * @return Object */ - public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader); - } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/AlignmentAnnotations.java b/src/org/vamsas/objects/core/AlignmentAnnotations.java index 5b62ccd..fd5fece 100755 --- a/src/org/vamsas/objects/core/AlignmentAnnotations.java +++ b/src/org/vamsas/objects/core/AlignmentAnnotations.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -75,8 +75,7 @@ public class AlignmentAnnotations implements java.io.Serializable { //- Constructors -/ //----------------/ - public AlignmentAnnotations() - { + public AlignmentAnnotations() { super(); _annotationElementList = new Vector(); } //-- org.vamsas.objects.core.AlignmentAnnotations() @@ -147,7 +146,7 @@ public class AlignmentAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index); @@ -332,7 +331,7 @@ public class AlignmentAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _annotationElementList.setElementAt(vAnnotationElement, index); } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) @@ -410,13 +409,13 @@ public class AlignmentAnnotations implements java.io.Serializable { * * * @param reader - * @return AlignmentAnnotations + * @return Object */ - public static org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotations.class, reader); - } //-- org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java index fe187b6..1d95f72 100755 --- a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java +++ b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //- Constructors -/ //----------------/ - public AlignmentAnnotationsDescriptor() - { + public AlignmentAnnotationsDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "AlignmentAnnotations"; @@ -62,13 +61,13 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -94,10 +93,9 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X 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 @@ -111,7 +109,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //-- _id desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -132,9 +130,8 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X 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 @@ -146,7 +143,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //-- _annotationElementList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -167,7 +164,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.AnnotationElement(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -183,7 +180,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -204,7 +201,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -223,7 +220,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -244,7 +241,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -262,7 +259,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X desc.setValidator(fieldValidator); //-- _provenance desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -283,7 +280,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Provenance(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java index 46c8c21..c02d0e7 100755 --- a/src/org/vamsas/objects/core/AlignmentDescriptor.java +++ b/src/org/vamsas/objects/core/AlignmentDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc //- Constructors -/ //----------------/ - public AlignmentDescriptor() - { + public AlignmentDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "Alignment"; @@ -62,14 +61,14 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,10 +89,9 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc 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 @@ -107,7 +105,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc desc.setValidator(fieldValidator); //-- _aligned desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -135,9 +133,8 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _aligned @@ -150,7 +147,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc //-- _id desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -171,9 +168,8 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc 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 @@ -185,7 +181,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc //-- _alignmentAnnotationsList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotations.class, "_alignmentAnnotationsList", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -206,7 +202,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.AlignmentAnnotations(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -220,7 +216,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc desc.setValidator(fieldValidator); //-- _treeList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -241,7 +237,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Tree(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -255,7 +251,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc desc.setValidator(fieldValidator); //-- _alignmentSequenceList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -276,7 +272,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.AlignmentSequence(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -291,7 +287,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc desc.setValidator(fieldValidator); //-- _provenance desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -312,7 +308,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Provenance(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java index 52ceee2..dcde8c4 100755 --- a/src/org/vamsas/objects/core/AlignmentSequence.java +++ b/src/org/vamsas/objects/core/AlignmentSequence.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -50,8 +50,7 @@ implements java.io.Serializable //- Constructors -/ //----------------/ - public AlignmentSequence() - { + public AlignmentSequence() { super(); } //-- org.vamsas.objects.core.AlignmentSequence() @@ -154,13 +153,13 @@ implements java.io.Serializable * * * @param reader - * @return SequenceType + * @return Object */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java index 4a722b8..c50f916 100755 --- a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java +++ b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,21 +53,20 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc //- Constructors -/ //----------------/ - public AlignmentSequenceDescriptor() - { + public AlignmentSequenceDescriptor() { super(); setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor()); nsURI = "http://www.vamsas.org"; xmlName = "alignmentSequence"; org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -88,9 +87,8 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc 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 @@ -101,7 +99,7 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc //-- _refid desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute); desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -122,10 +120,9 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc public java.lang.Object newInstance( java.lang.Object parent ) { return new java.lang.Object(); } - }; + } ); desc.setHandler(handler); desc.setRequired(true); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _refid diff --git a/src/org/vamsas/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java index b0d2682..f9c0e8c 100755 --- a/src/org/vamsas/objects/core/AnnotationElement.java +++ b/src/org/vamsas/objects/core/AnnotationElement.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -78,8 +78,7 @@ public class AnnotationElement implements java.io.Serializable { //- Constructors -/ //----------------/ - public AnnotationElement() - { + public AnnotationElement() { super(); } //-- org.vamsas.objects.core.AnnotationElement() @@ -311,13 +310,13 @@ public class AnnotationElement implements java.io.Serializable { * * * @param reader - * @return AnnotationElement + * @return Object */ - public static org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader); - } //-- org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java index d02838b..24c55e6 100755 --- a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java +++ b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC //- Constructors -/ //----------------/ - public AnnotationElementDescriptor() - { + public AnnotationElementDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "annotationElement"; @@ -62,13 +61,13 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -94,24 +93,23 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC 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 - IntegerValidator typeValidator= new IntegerValidator(); + IntegerValidator typeValidator = new IntegerValidator(); 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -132,9 +130,8 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC 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 @@ -147,7 +144,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -168,7 +165,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -185,7 +182,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -206,7 +203,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -223,7 +220,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -244,7 +241,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -261,7 +258,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC desc.setValidator(fieldValidator); //-- _value desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -289,7 +286,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); diff --git a/src/org/vamsas/objects/core/Application.java b/src/org/vamsas/objects/core/Application.java index 94b8e84..5283c35 100755 --- a/src/org/vamsas/objects/core/Application.java +++ b/src/org/vamsas/objects/core/Application.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -65,8 +65,7 @@ public class Application implements java.io.Serializable { //- Constructors -/ //----------------/ - public Application() - { + public Application() { super(); _userList = new Vector(); } //-- org.vamsas.objects.core.Application() @@ -161,7 +160,7 @@ public class Application implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("getUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.User) _userList.elementAt(index); @@ -320,7 +319,7 @@ public class Application implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("setUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _userList.setElementAt(vUser, index); } //-- void setUser(int, org.vamsas.objects.core.User) @@ -357,13 +356,13 @@ public class Application implements java.io.Serializable { * * * @param reader - * @return Application + * @return Object */ - public static org.vamsas.objects.core.Application unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Application) Unmarshaller.unmarshal(org.vamsas.objects.core.Application.class, reader); - } //-- org.vamsas.objects.core.Application unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/ApplicationData.java b/src/org/vamsas/objects/core/ApplicationData.java index d775ea5..bf61e7b 100755 --- a/src/org/vamsas/objects/core/ApplicationData.java +++ b/src/org/vamsas/objects/core/ApplicationData.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -45,8 +45,7 @@ public class ApplicationData implements java.io.Serializable { //- Constructors -/ //----------------/ - public ApplicationData() - { + public ApplicationData() { super(); _applicationList = new Vector(); } //-- org.vamsas.objects.core.ApplicationData() @@ -108,7 +107,7 @@ public class ApplicationData implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _applicationList.size())) { - throw new IndexOutOfBoundsException("getApplication: Index value '"+index+"' not in range [0.."+_applicationList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Application) _applicationList.elementAt(index); @@ -226,7 +225,7 @@ public class ApplicationData implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _applicationList.size())) { - throw new IndexOutOfBoundsException("setApplication: Index value '"+index+"' not in range [0.."+_applicationList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _applicationList.setElementAt(vApplication, index); } //-- void setApplication(int, org.vamsas.objects.core.Application) @@ -253,13 +252,13 @@ public class ApplicationData implements java.io.Serializable { * * * @param reader - * @return ApplicationData + * @return Object */ - public static org.vamsas.objects.core.ApplicationData unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader); - } //-- org.vamsas.objects.core.ApplicationData unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java index b7ef5b5..ac7225f 100755 --- a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java +++ b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla //- Constructors -/ //----------------/ - public ApplicationDataDescriptor() - { + public ApplicationDataDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "ApplicationData"; @@ -62,7 +61,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors @@ -70,7 +69,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla //-- _applicationList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Application.class, "_applicationList", "Application", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -91,7 +90,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Application(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); diff --git a/src/org/vamsas/objects/core/ApplicationDescriptor.java b/src/org/vamsas/objects/core/ApplicationDescriptor.java index e6be012..ef61bd7 100755 --- a/src/org/vamsas/objects/core/ApplicationDescriptor.java +++ b/src/org/vamsas/objects/core/ApplicationDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //- Constructors -/ //----------------/ - public ApplicationDescriptor() - { + public ApplicationDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "Application"; @@ -62,14 +61,14 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,10 +89,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe 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: _version @@ -108,7 +106,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -129,10 +127,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe 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 @@ -147,7 +144,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- _urn desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -168,10 +165,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe 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: _urn @@ -186,7 +182,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- _data desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -207,10 +203,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe 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: _data @@ -226,7 +221,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- _userList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -247,7 +242,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.User(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java index b3d6671..4de0939 100755 --- a/src/org/vamsas/objects/core/DataSet.java +++ b/src/org/vamsas/objects/core/DataSet.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -70,8 +70,7 @@ public class DataSet implements java.io.Serializable { //- Constructors -/ //----------------/ - public DataSet() - { + public DataSet() { super(); _sequenceList = new Vector(); _dataSetAnnotationsList = new Vector(); @@ -253,7 +252,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index); @@ -301,7 +300,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index); @@ -371,7 +370,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index); @@ -419,7 +418,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); @@ -609,7 +608,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _alignmentList.setElementAt(vAlignment, index); } //-- void setAlignment(int, org.vamsas.objects.core.Alignment) @@ -643,7 +642,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index); } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) @@ -697,7 +696,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _sequenceList.setElementAt(vSequence, index); } //-- void setSequence(int, org.vamsas.objects.core.Sequence) @@ -731,7 +730,7 @@ public class DataSet implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _treeList.setElementAt(vTree, index); } //-- void setTree(int, org.vamsas.objects.core.Tree) @@ -758,13 +757,13 @@ public class DataSet implements java.io.Serializable { * * * @param reader - * @return DataSet + * @return Object */ - public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader); - } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/DataSetAnnotations.java b/src/org/vamsas/objects/core/DataSetAnnotations.java index 42d684a..c8c6a4e 100755 --- a/src/org/vamsas/objects/core/DataSetAnnotations.java +++ b/src/org/vamsas/objects/core/DataSetAnnotations.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -43,12 +43,22 @@ public class DataSetAnnotations implements java.io.Serializable { /** * Field _end */ - private java.lang.String _end; + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; /** * Field _begin */ - private java.lang.String _begin; + private int _begin; + + /** + * keeps track of state for field: _begin + */ + private boolean _has_begin; /** * Field _seqRef @@ -85,8 +95,7 @@ public class DataSetAnnotations implements java.io.Serializable { //- Constructors -/ //----------------/ - public DataSetAnnotations() - { + public DataSetAnnotations() { super(); _annotationElementList = new Vector(); _provenanceList = new Vector(); @@ -152,6 +161,24 @@ public class DataSetAnnotations implements java.io.Serializable { } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) /** + * Method deleteBegin + * + */ + public void deleteBegin() + { + this._has_begin= false; + } //-- void deleteBegin() + + /** + * Method deleteEnd + * + */ + public void deleteEnd() + { + this._has_end= false; + } //-- void deleteEnd() + + /** * Method enumerateAnnotationElement * * @@ -188,7 +215,7 @@ public class DataSetAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index); @@ -226,13 +253,13 @@ public class DataSetAnnotations implements java.io.Serializable { /** * Returns the value of field 'begin'. * - * @return String + * @return int * @return the value of field 'begin'. */ - public java.lang.String getBegin() + public int getBegin() { return this._begin; - } //-- java.lang.String getBegin() + } //-- int getBegin() /** * Returns the value of field 'description'. @@ -248,13 +275,13 @@ public class DataSetAnnotations implements java.io.Serializable { /** * Returns the value of field 'end'. * - * @return String + * @return int * @return the value of field 'end'. */ - public java.lang.String getEnd() + public int getEnd() { return this._end; - } //-- java.lang.String getEnd() + } //-- int getEnd() /** * Returns the value of field 'id'. @@ -280,7 +307,7 @@ public class DataSetAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _provenanceList.size())) { - throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index); @@ -349,6 +376,30 @@ public class DataSetAnnotations implements java.io.Serializable { } //-- java.lang.String getType() /** + * Method hasBegin + * + * + * + * @return boolean + */ + public boolean hasBegin() + { + return this._has_begin; + } //-- boolean hasBegin() + + /** + * Method hasEnd + * + * + * + * @return boolean + */ + public boolean hasEnd() + { + return this._has_end; + } //-- boolean hasEnd() + + /** * Method isValid * * @@ -455,7 +506,7 @@ public class DataSetAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _annotationElementList.setElementAt(vAnnotationElement, index); } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) @@ -481,10 +532,11 @@ public class DataSetAnnotations implements java.io.Serializable { * * @param begin the value of field 'begin'. */ - public void setBegin(java.lang.String begin) + public void setBegin(int begin) { this._begin = begin; - } //-- void setBegin(java.lang.String) + this._has_begin = true; + } //-- void setBegin(int) /** * Sets the value of field 'description'. @@ -501,10 +553,11 @@ public class DataSetAnnotations implements java.io.Serializable { * * @param end the value of field 'end'. */ - public void setEnd(java.lang.String end) + public void setEnd(int end) { this._end = end; - } //-- void setEnd(java.lang.String) + this._has_end = true; + } //-- void setEnd(int) /** * Sets the value of field 'id'. @@ -529,7 +582,7 @@ public class DataSetAnnotations implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _provenanceList.size())) { - throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _provenanceList.setElementAt(vProvenance, index); } //-- void setProvenance(int, org.vamsas.objects.core.Provenance) @@ -586,13 +639,13 @@ public class DataSetAnnotations implements java.io.Serializable { * * * @param reader - * @return DataSetAnnotations + * @return Object */ - public static org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader); - } //-- org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java index fdebfc2..9dcbb86 100755 --- a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java +++ b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML //- Constructors -/ //----------------/ - public DataSetAnnotationsDescriptor() - { + public DataSetAnnotationsDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "DataSetAnnotations"; @@ -62,14 +61,14 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,10 +89,9 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML 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 @@ -106,21 +104,25 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML } desc.setValidator(fieldValidator); //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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 { DataSetAnnotations target = (DataSetAnnotations) object; - return target.getEnd(); + 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 { DataSetAnnotations target = (DataSetAnnotations) object; - target.setEnd( (java.lang.String) value); + // 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()); @@ -129,37 +131,39 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML 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 - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); + IntegerValidator typeValidator = new IntegerValidator(); fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- _begin - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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 { DataSetAnnotations target = (DataSetAnnotations) object; - return target.getBegin(); + 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 { DataSetAnnotations target = (DataSetAnnotations) object; - target.setBegin( (java.lang.String) value); + // 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()); @@ -168,25 +172,23 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML 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 - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); + IntegerValidator typeValidator = new IntegerValidator(); fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- _seqRef desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute); desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -207,10 +209,9 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML public java.lang.Object newInstance( java.lang.Object parent ) { return new java.lang.Object(); } - }; + } ); desc.setHandler(handler); desc.setRequired(true); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _seqRef @@ -222,7 +223,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML //-- _id desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -243,9 +244,8 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML 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 @@ -258,7 +258,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -279,7 +279,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -296,7 +296,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML //-- _status desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -317,7 +317,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -333,7 +333,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML desc.setValidator(fieldValidator); //-- _annotationElementList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -354,7 +354,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.AnnotationElement(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -368,7 +368,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML desc.setValidator(fieldValidator); //-- _provenanceList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenanceList", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -389,7 +389,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Provenance(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/DataSetDescriptor.java b/src/org/vamsas/objects/core/DataSetDescriptor.java index d938f51..6651358 100755 --- a/src/org/vamsas/objects/core/DataSetDescriptor.java +++ b/src/org/vamsas/objects/core/DataSetDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri //- Constructors -/ //----------------/ - public DataSetDescriptor() - { + public DataSetDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "DataSet"; @@ -62,14 +61,14 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,9 +89,8 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri 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 @@ -104,7 +102,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri //-- _sequenceList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -125,7 +123,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Sequence(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -140,7 +138,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri desc.setValidator(fieldValidator); //-- _dataSetAnnotationsList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -161,7 +159,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.DataSetAnnotations(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -175,7 +173,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri desc.setValidator(fieldValidator); //-- _alignmentList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -196,7 +194,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Alignment(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -210,7 +208,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri desc.setValidator(fieldValidator); //-- _treeList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -231,7 +229,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Tree(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -245,7 +243,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri desc.setValidator(fieldValidator); //-- _provenance desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -266,7 +264,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Provenance(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java index 47d57f2..10109b2 100755 --- a/src/org/vamsas/objects/core/DbRef.java +++ b/src/org/vamsas/objects/core/DbRef.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -36,17 +36,17 @@ public class DbRef implements java.io.Serializable { /** * Field _source */ - private java.lang.Object _source; + private java.lang.String _source; /** * Field _version */ - private java.lang.Object _version; + private java.lang.String _version; /** * Field _accessionId */ - private java.lang.Object _accessionId; + private java.lang.String _accessionId; /** * Field _id @@ -58,8 +58,7 @@ public class DbRef implements java.io.Serializable { //- Constructors -/ //----------------/ - public DbRef() - { + public DbRef() { super(); } //-- org.vamsas.objects.core.DbRef() @@ -71,13 +70,13 @@ public class DbRef implements java.io.Serializable { /** * Returns the value of field 'accessionId'. * - * @return Object + * @return String * @return the value of field 'accessionId'. */ - public java.lang.Object getAccessionId() + public java.lang.String getAccessionId() { return this._accessionId; - } //-- java.lang.Object getAccessionId() + } //-- java.lang.String getAccessionId() /** * Returns the value of field 'id'. @@ -93,24 +92,24 @@ public class DbRef implements java.io.Serializable { /** * Returns the value of field 'source'. * - * @return Object + * @return String * @return the value of field 'source'. */ - public java.lang.Object getSource() + public java.lang.String getSource() { return this._source; - } //-- java.lang.Object getSource() + } //-- java.lang.String getSource() /** * Returns the value of field 'version'. * - * @return Object + * @return String * @return the value of field 'version'. */ - public java.lang.Object getVersion() + public java.lang.String getVersion() { return this._version; - } //-- java.lang.Object getVersion() + } //-- java.lang.String getVersion() /** * Method isValid @@ -163,10 +162,10 @@ public class DbRef implements java.io.Serializable { * * @param accessionId the value of field 'accessionId'. */ - public void setAccessionId(java.lang.Object accessionId) + public void setAccessionId(java.lang.String accessionId) { this._accessionId = accessionId; - } //-- void setAccessionId(java.lang.Object) + } //-- void setAccessionId(java.lang.String) /** * Sets the value of field 'id'. @@ -183,20 +182,20 @@ public class DbRef implements java.io.Serializable { * * @param source the value of field 'source'. */ - public void setSource(java.lang.Object source) + public void setSource(java.lang.String source) { this._source = source; - } //-- void setSource(java.lang.Object) + } //-- void setSource(java.lang.String) /** * Sets the value of field 'version'. * * @param version the value of field 'version'. */ - public void setVersion(java.lang.Object version) + public void setVersion(java.lang.String version) { this._version = version; - } //-- void setVersion(java.lang.Object) + } //-- void setVersion(java.lang.String) /** * Method unmarshal @@ -204,13 +203,13 @@ public class DbRef implements java.io.Serializable { * * * @param reader - * @return DbRef + * @return Object */ - public static org.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader); - } //-- org.vamsas.objects.core.DbRef unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java index 726c0cb..e679843 100755 --- a/src/org/vamsas/objects/core/DbRefDescriptor.java +++ b/src/org/vamsas/objects/core/DbRefDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,19 +53,19 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript //- Constructors -/ //----------------/ - public DbRefDescriptor() - { + public DbRefDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "dbRef"; org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors //-- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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 { @@ -77,28 +77,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript { try { DbRef target = (DbRef) object; - target.setSource( (java.lang.Object) value); + 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 new java.lang.Object(); + return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _source fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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 { @@ -110,28 +113,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript { try { DbRef target = (DbRef) object; - target.setVersion( (java.lang.Object) value); + 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 new java.lang.Object(); + return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _version fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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 { @@ -143,29 +149,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript { try { DbRef target = (DbRef) object; - target.setAccessionId( (java.lang.Object) value); + 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 new java.lang.Object(); + return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _accessionId fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -186,9 +194,8 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript 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 diff --git a/src/org/vamsas/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java index 8232a43..9e41a3c 100755 --- a/src/org/vamsas/objects/core/Entry.java +++ b/src/org/vamsas/objects/core/Entry.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -58,8 +58,7 @@ public class Entry implements java.io.Serializable { //- Constructors -/ //----------------/ - public Entry() - { + public Entry() { super(); } //-- org.vamsas.objects.core.Entry() @@ -204,13 +203,13 @@ public class Entry implements java.io.Serializable { * * * @param reader - * @return Entry + * @return Object */ - public static org.vamsas.objects.core.Entry unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader); - } //-- org.vamsas.objects.core.Entry unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java index 981ee47..b404b3a 100755 --- a/src/org/vamsas/objects/core/EntryDescriptor.java +++ b/src/org/vamsas/objects/core/EntryDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript //- Constructors -/ //----------------/ - public EntryDescriptor() - { + public EntryDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "entry"; @@ -62,14 +61,14 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,9 +89,8 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript 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 @@ -105,7 +103,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript //-- _user desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -126,7 +124,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -145,7 +143,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript //-- _action desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -166,7 +164,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -184,7 +182,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript desc.setValidator(fieldValidator); //-- _date desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -205,7 +203,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript public java.lang.Object newInstance( java.lang.Object parent ) { return new org.exolab.castor.types.Date(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java index c0988ec..3c59ad7 100755 --- a/src/org/vamsas/objects/core/Newick.java +++ b/src/org/vamsas/objects/core/Newick.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class Newick implements java.io.Serializable { //- Constructors -/ //----------------/ - public Newick() - { + public Newick() { super(); setContent(""); } //-- org.vamsas.objects.core.Newick() @@ -181,13 +180,13 @@ public class Newick implements java.io.Serializable { * * * @param reader - * @return Newick + * @return Object */ - public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader); - } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java index 97ea4ff..474da72 100755 --- a/src/org/vamsas/objects/core/NewickDescriptor.java +++ b/src/org/vamsas/objects/core/NewickDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,18 +53,17 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //- Constructors -/ //----------------/ - public NewickDescriptor() - { + public NewickDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "newick"; org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -85,7 +84,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); addFieldDescriptor(desc); @@ -102,7 +101,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -123,9 +122,8 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _title @@ -139,7 +137,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //-- _id desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -160,9 +158,8 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip 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 diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java index 360f035..0011b05 100755 --- a/src/org/vamsas/objects/core/Provenance.java +++ b/src/org/vamsas/objects/core/Provenance.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -45,8 +45,7 @@ public class Provenance implements java.io.Serializable { //- Constructors -/ //----------------/ - public Provenance() - { + public Provenance() { super(); _entryList = new Vector(); } //-- org.vamsas.objects.core.Provenance() @@ -108,7 +107,7 @@ public class Provenance implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Entry) _entryList.elementAt(index); @@ -226,7 +225,7 @@ public class Provenance implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _entryList.setElementAt(vEntry, index); } //-- void setEntry(int, org.vamsas.objects.core.Entry) @@ -253,13 +252,13 @@ public class Provenance implements java.io.Serializable { * * * @param reader - * @return Provenance + * @return Object */ - public static org.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader); - } //-- org.vamsas.objects.core.Provenance unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java index 480ee5f..17b283c 100755 --- a/src/org/vamsas/objects/core/ProvenanceDescriptor.java +++ b/src/org/vamsas/objects/core/ProvenanceDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes //- Constructors -/ //----------------/ - public ProvenanceDescriptor() - { + public ProvenanceDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "Provenance"; @@ -62,7 +61,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors @@ -70,7 +69,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes //-- _entryList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -91,7 +90,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Entry(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java index daf6657..2a7e0ec 100755 --- a/src/org/vamsas/objects/core/Sequence.java +++ b/src/org/vamsas/objects/core/Sequence.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -57,8 +57,7 @@ implements java.io.Serializable //- Constructors -/ //----------------/ - public Sequence() - { + public Sequence() { super(); _dbRefList = new Vector(); } //-- org.vamsas.objects.core.Sequence() @@ -120,7 +119,7 @@ implements java.io.Serializable { //-- check bounds for index if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); @@ -260,7 +259,7 @@ implements java.io.Serializable { //-- check bounds for index if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _dbRefList.setElementAt(vDbRef, index); } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) @@ -307,13 +306,13 @@ implements java.io.Serializable * * * @param reader - * @return SequenceType + * @return Object */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java index 6f25ae1..e17ff8f 100755 --- a/src/org/vamsas/objects/core/SequenceDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc //- Constructors -/ //----------------/ - public SequenceDescriptor() - { + public SequenceDescriptor() { super(); setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor()); nsURI = "http://www.vamsas.org"; @@ -63,14 +62,14 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -91,10 +90,9 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new java.lang.String(); } - }; + } ); desc.setHandler(handler); desc.setRequired(true); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _id @@ -106,7 +104,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc //-- _dictionary desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -127,9 +125,8 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _dictionary @@ -144,7 +141,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc //-- _dbRefList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -165,7 +162,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.DbRef(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java index 7ecd190..957edb5 100755 --- a/src/org/vamsas/objects/core/SequenceType.java +++ b/src/org/vamsas/objects/core/SequenceType.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -68,8 +68,7 @@ public class SequenceType implements java.io.Serializable { //- Constructors -/ //----------------/ - public SequenceType() - { + public SequenceType() { super(); } //-- org.vamsas.objects.core.SequenceType() @@ -258,13 +257,13 @@ public class SequenceType implements java.io.Serializable { * * * @param reader - * @return SequenceType + * @return Object */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java index eda209f..6090776 100755 --- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD //- Constructors -/ //----------------/ - public SequenceTypeDescriptor() - { + public SequenceTypeDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "SequenceType"; @@ -62,13 +61,13 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -94,23 +93,22 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD 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 - IntegerValidator typeValidator= new IntegerValidator(); + IntegerValidator typeValidator = new IntegerValidator(); fieldValidator.setValidator(typeValidator); } 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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -136,17 +134,16 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD 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 - IntegerValidator typeValidator= new IntegerValidator(); + IntegerValidator typeValidator = new IntegerValidator(); fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); @@ -155,7 +152,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -176,7 +173,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -195,7 +192,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -216,7 +213,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java index f18cd05..1e37459 100755 --- a/src/org/vamsas/objects/core/Tree.java +++ b/src/org/vamsas/objects/core/Tree.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -60,8 +60,7 @@ public class Tree implements java.io.Serializable { //- Constructors -/ //----------------/ - public Tree() - { + public Tree() { super(); _newickList = new Vector(); } //-- org.vamsas.objects.core.Tree() @@ -134,7 +133,7 @@ public class Tree implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Newick) _newickList.elementAt(index); @@ -284,7 +283,7 @@ public class Tree implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _newickList.setElementAt(vNewick, index); } //-- void setNewick(int, org.vamsas.objects.core.Newick) @@ -331,13 +330,13 @@ public class Tree implements java.io.Serializable { * * * @param reader - * @return Tree + * @return Object */ - public static org.vamsas.objects.core.Tree unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader); - } //-- org.vamsas.objects.core.Tree unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java index bd1ecb0..17c7ff6 100755 --- a/src/org/vamsas/objects/core/TreeDescriptor.java +++ b/src/org/vamsas/objects/core/TreeDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //- Constructors -/ //----------------/ - public TreeDescriptor() - { + public TreeDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "Tree"; @@ -62,14 +61,14 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,9 +89,8 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto 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 @@ -105,7 +103,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //-- _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() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -126,7 +124,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(false); @@ -142,7 +140,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto desc.setValidator(fieldValidator); //-- _newickList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -163,7 +161,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Newick(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); @@ -178,7 +176,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto desc.setValidator(fieldValidator); //-- _provenance desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -199,7 +197,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Provenance(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setRequired(true); diff --git a/src/org/vamsas/objects/core/User.java b/src/org/vamsas/objects/core/User.java index 598bceb..16455e9 100755 --- a/src/org/vamsas/objects/core/User.java +++ b/src/org/vamsas/objects/core/User.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class User implements java.io.Serializable { //- Constructors -/ //----------------/ - public User() - { + public User() { super(); } //-- org.vamsas.objects.core.User() @@ -178,13 +177,13 @@ public class User implements java.io.Serializable { * * * @param reader - * @return User + * @return Object */ - public static org.vamsas.objects.core.User unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader); - } //-- org.vamsas.objects.core.User unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java index f318dde..7e50932 100755 --- a/src/org/vamsas/objects/core/UserDescriptor.java +++ b/src/org/vamsas/objects/core/UserDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,20 +53,19 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //- Constructors -/ //----------------/ - public UserDescriptor() - { + public UserDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "User"; org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors //-- _fullname desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -87,9 +86,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _fullname @@ -103,7 +101,7 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //-- _organization desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -124,9 +122,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _organization @@ -140,7 +137,7 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto //-- _data desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -161,9 +158,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public java.lang.Object newInstance( java.lang.Object parent ) { return null; } - }; + } ); desc.setHandler(handler); - desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _data diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java index 8d9b765..e419b5c 100755 --- a/src/org/vamsas/objects/core/VAMSAS.java +++ b/src/org/vamsas/objects/core/VAMSAS.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -55,8 +55,7 @@ public class VAMSAS implements java.io.Serializable { //- Constructors -/ //----------------/ - public VAMSAS() - { + public VAMSAS() { super(); _treeList = new Vector(); _dataSetList = new Vector(); @@ -158,7 +157,7 @@ public class VAMSAS implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index); @@ -217,7 +216,7 @@ public class VAMSAS implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); @@ -359,7 +358,7 @@ public class VAMSAS implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _dataSetList.setElementAt(vDataSet, index); } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) @@ -403,7 +402,7 @@ public class VAMSAS implements java.io.Serializable { { //-- check bounds for index if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + throw new IndexOutOfBoundsException(); } _treeList.setElementAt(vTree, index); } //-- void setTree(int, org.vamsas.objects.core.Tree) @@ -430,13 +429,13 @@ public class VAMSAS implements java.io.Serializable { * * * @param reader - * @return VAMSAS + * @return Object */ - public static org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader) + public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader); - } //-- org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java index 053b0e1..40c8f6a 100755 --- a/src/org/vamsas/objects/core/VAMSASDescriptor.java +++ b/src/org/vamsas/objects/core/VAMSASDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 0.9.6, using an XML * Schema. * $Id$ */ @@ -53,8 +53,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //- Constructors -/ //----------------/ - public VAMSASDescriptor() - { + public VAMSASDescriptor() { super(); nsURI = "http://www.vamsas.org"; xmlName = "VAMSAS"; @@ -62,14 +61,14 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //-- set grouping compositor setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.XMLFieldHandler 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); this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -90,9 +89,8 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip 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 @@ -104,7 +102,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip //-- _treeList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -125,7 +123,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.Tree(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); @@ -139,7 +137,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip desc.setValidator(fieldValidator); //-- _dataSetList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { + handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { @@ -160,7 +158,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip public java.lang.Object newInstance( java.lang.Object parent ) { return new org.vamsas.objects.core.DataSet(); } - }; + } ); desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true);