From: jprocter Date: Mon, 19 Sep 2005 23:31:25 +0000 (+0000) Subject: updated to castor-0.9.9M2 and added some comments X-Git-Tag: Release_0.2~489 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a54f7d71affe4e9cd7a7b0f6137e44f5b82b7a9d;p=vamsas.git updated to castor-0.9.9M2 and added some comments git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@31 be28352e-c001-0410-b1a7-c7978e42abec --- diff --git a/lib/castor-0.9.9M2-xml.jar b/lib/castor-0.9.9M2-xml.jar new file mode 100644 index 0000000..300fce5 Binary files /dev/null and b/lib/castor-0.9.9M2-xml.jar differ diff --git a/lib/castor-0.9.9M1.jar b/lib/castor-0.9.9M2.jar similarity index 87% rename from lib/castor-0.9.9M1.jar rename to lib/castor-0.9.9M2.jar index 2d303b6..9d2239f 100644 Binary files a/lib/castor-0.9.9M1.jar and b/lib/castor-0.9.9M2.jar differ diff --git a/lib/jdbc-se2.0.jar b/lib/jdbc-se2.0.jar new file mode 100644 index 0000000..7b6e322 Binary files /dev/null and b/lib/jdbc-se2.0.jar differ diff --git a/lib/jta1.0.1.jar b/lib/jta1.0.1.jar new file mode 100644 index 0000000..b56c2d8 Binary files /dev/null and b/lib/jta1.0.1.jar differ diff --git a/src/org/vamsas/client/ClientDocument.java b/src/org/vamsas/client/ClientDocument.java index 4a78bd4..2a3ce45 100644 --- a/src/org/vamsas/client/ClientDocument.java +++ b/src/org/vamsas/client/ClientDocument.java @@ -11,32 +11,35 @@ import java.util.Hashtable; * to a specified ClientHandle's information. */ public class ClientDocument implements IClientDocument { - /* (non-Javadoc) + IClient vorba; + /* (non-Javadoc) * @see org.vamsas.client.IClientDocument#getApplicationData() */ public byte[] getApplicationData() { - // TODO Auto-generated method stub + // Look up client byte stash using client and user handle + return null; } /* (non-Javadoc) * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId) */ public object getObject(VorbaId id) { - // TODO Auto-generated method stub + // look up id in document object + // retrieve object and return return null; } /* (non-Javadoc) * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[]) */ public object[] getObjects(VorbaId[] ids) { - // TODO Auto-generated method stub + // getObject in bulk return null; } /* (non-Javadoc) * @see org.vamsas.client.IClientDocument#getVamsasRoots() */ public object[] getVamsasRoots() { - // TODO Auto-generated method stub + // extract root objects return null; } /* (non-Javadoc) diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr index ce4c376..415b24d 100644 --- a/src/org/vamsas/objects/core/.castor.cdr +++ b/src/org/vamsas/objects/core/.castor.cdr @@ -1,18 +1,20 @@ -- listing properties -- -org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte... -org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno... org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor -org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr... +org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes... +org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD... +org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte... +org.vamsas.objects.core.TreeType=org.vamsas.objects.core.TreeTypeDescr... org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle... +org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ... +org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc... +org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor +org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn... +org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe... +org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor +org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr... org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr... org.vamsas.objects.core.Entry=org.vamsas.objects.core.EntryDescriptor -org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD... -org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor org.vamsas.objects.core.SequenceSet=org.vamsas.objects.core.SequenceSetDe... -org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor org.vamsas.objects.core.ApplicationData=org.vamsas.objects.core.ApplicationDa... -org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe... -org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes... -org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ... -org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc... -org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn... +org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno... +org.vamsas.objects.core.Dendro=org.vamsas.objects.core.DendroDescriptor diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java index edd0391..b9fa81c 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/AlignmentAnnotations.java b/src/org/vamsas/objects/core/AlignmentAnnotations.java index 7b262d2..4d5f8fa 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -48,6 +48,11 @@ implements java.io.Serializable private boolean _has_graph; /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _annotationElementList */ private java.util.Vector _annotationElementList; @@ -152,6 +157,13 @@ implements java.io.Serializable return false; if (this._has_graph != temp._has_graph) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._annotationElementList != null) { if (temp._annotationElementList == null) return false; else if (!(this._annotationElementList.equals(temp._annotationElementList))) @@ -256,6 +268,17 @@ implements java.io.Serializable } //-- boolean getGraph() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'label'. * * @return String @@ -415,6 +438,16 @@ implements java.io.Serializable } //-- void setGraph(boolean) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'label'. * * @param label the value of field 'label'. diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java index d680cd8..3ded2eb 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -108,6 +108,40 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _annotationElementList diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java index 497eb37..8e20b93 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java index df55b39..91fd691 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -36,9 +36,9 @@ implements java.io.Serializable //--------------------------/ /** - * Field _id + * Field _refid */ - private java.lang.Object _id; + private java.lang.Object _refid; //----------------/ @@ -72,12 +72,12 @@ implements java.io.Serializable if (obj instanceof AlignmentSequence) { AlignmentSequence temp = (AlignmentSequence)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) + if (this._refid != null) { + if (temp._refid == null) return false; + else if (!(this._refid.equals(temp._refid))) return false; } - else if (temp._id != null) + else if (temp._refid != null) return false; return true; } @@ -85,15 +85,15 @@ implements java.io.Serializable } //-- boolean equals(java.lang.Object) /** - * Returns the value of field 'id'. + * Returns the value of field 'refid'. * * @return Object - * @return the value of field 'id'. + * @return the value of field 'refid'. */ - public java.lang.Object getId() + public java.lang.Object getRefid() { - return this._id; - } //-- java.lang.Object getId() + return this._refid; + } //-- java.lang.Object getRefid() /** * Method isValid @@ -142,14 +142,14 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** - * Sets the value of field 'id'. + * Sets the value of field 'refid'. * - * @param id the value of field 'id'. + * @param refid the value of field 'refid'. */ - public void setId(java.lang.Object id) + public void setRefid(java.lang.Object refid) { - this._id = id; - } //-- void setId(java.lang.Object) + this._refid = refid; + } //-- void setRefid(java.lang.Object) /** * Method unmarshal diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java index dd1680a..b49e045 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -64,22 +64,22 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + //-- _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() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { AlignmentSequence target = (AlignmentSequence) object; - return target.getId(); + return target.getRefid(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { AlignmentSequence target = (AlignmentSequence) object; - target.setId( (java.lang.Object) value); + target.setRefid( (java.lang.Object) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -94,7 +94,7 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc desc.setMultivalued(false); addFieldDescriptor(desc); - //-- validation code for: _id + //-- validation code for: _refid fieldValidator = new org.exolab.castor.xml.FieldValidator(); fieldValidator.setMinOccurs(1); { //-- local scope diff --git a/src/org/vamsas/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java index 534eb9c..8d72277 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -46,6 +46,11 @@ implements java.io.Serializable private boolean _has_position; /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _displayCharacter */ private java.lang.String _displayCharacter; @@ -124,6 +129,13 @@ implements java.io.Serializable return false; if (this._has_position != temp._has_position) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._displayCharacter != null) { if (temp._displayCharacter == null) return false; else if (!(this._displayCharacter.equals(temp._displayCharacter))) @@ -177,6 +189,17 @@ implements java.io.Serializable } //-- java.lang.String getDisplayCharacter() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'position'. * * @return int @@ -300,6 +323,16 @@ implements java.io.Serializable } //-- void setDisplayCharacter(java.lang.String) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'position'. * * @param position the value of field 'position'. diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java index 419388a..9bc3e57 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -108,6 +108,40 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _displayCharacter diff --git a/src/org/vamsas/objects/core/Application.java b/src/org/vamsas/objects/core/Application.java index 261bffd..1b2659c 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -38,12 +38,22 @@ implements java.io.Serializable /** * Field _version */ - private java.lang.Object _version; + private java.lang.String _version; /** * Field _name */ - private java.lang.Object _name; + private java.lang.String _name; + + /** + * Field _session + */ + private java.lang.String _session; + + /** + * Field _data + */ + private java.lang.String _data; //----------------/ @@ -91,32 +101,68 @@ implements java.io.Serializable } else if (temp._name != null) return false; + if (this._session != null) { + if (temp._session == null) return false; + else if (!(this._session.equals(temp._session))) + return false; + } + else if (temp._session != null) + return false; + if (this._data != null) { + if (temp._data == null) return false; + else if (!(this._data.equals(temp._data))) + return false; + } + else if (temp._data != null) + return false; return true; } return false; } //-- boolean equals(java.lang.Object) /** + * Returns the value of field 'data'. + * + * @return String + * @return the value of field 'data'. + */ + public java.lang.String getData() + { + return this._data; + } //-- java.lang.String getData() + + /** * Returns the value of field 'name'. * - * @return Object + * @return String * @return the value of field 'name'. */ - public java.lang.Object getName() + public java.lang.String getName() { return this._name; - } //-- java.lang.Object getName() + } //-- java.lang.String getName() + + /** + * Returns the value of field 'session'. + * + * @return String + * @return the value of field 'session'. + */ + public java.lang.String getSession() + { + return this._session; + } //-- java.lang.String getSession() /** * 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 @@ -165,24 +211,44 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** + * Sets the value of field 'data'. + * + * @param data the value of field 'data'. + */ + public void setData(java.lang.String data) + { + this._data = data; + } //-- void setData(java.lang.String) + + /** * Sets the value of field 'name'. * * @param name the value of field 'name'. */ - public void setName(java.lang.Object name) + public void setName(java.lang.String name) { this._name = name; - } //-- void setName(java.lang.Object) + } //-- void setName(java.lang.String) + + /** + * Sets the value of field 'session'. + * + * @param session the value of field 'session'. + */ + public void setSession(java.lang.String session) + { + this._session = session; + } //-- void setSession(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 diff --git a/src/org/vamsas/objects/core/ApplicationData.java b/src/org/vamsas/objects/core/ApplicationData.java index 6e720b2..cd13be4 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java index 6386e8d..bf3e8ff 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/ApplicationDescriptor.java b/src/org/vamsas/objects/core/ApplicationDescriptor.java index 1b5b429..7b3a6a6 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -64,7 +64,8 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- initialize attribute descriptors //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); + 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 @@ -77,14 +78,14 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe { try { Application target = (Application) 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); @@ -94,10 +95,14 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- 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); //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException @@ -110,14 +115,14 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe { try { Application target = (Application) object; - target.setName( (java.lang.Object) value); + target.setName( (java.lang.String) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } } public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); + return null; } }; desc.setHandler(handler); @@ -127,6 +132,83 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe //-- validation code for: _name fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _session + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_session", "session", 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 + { + Application target = (Application) object; + return target.getSession(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Application target = (Application) object; + target.setSession( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _session + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Application target = (Application) object; + return target.getData(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Application target = (Application) object; + target.setData( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _data + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- initialize element descriptors diff --git a/src/org/vamsas/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java index c65d466..48b9a74 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -50,6 +50,11 @@ implements java.io.Serializable */ private java.lang.Object _accessionId; + /** + * Field _id + */ + private java.lang.String _id; + //----------------/ //- Constructors -/ @@ -103,6 +108,13 @@ implements java.io.Serializable } else if (temp._accessionId != null) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; return true; } return false; @@ -120,6 +132,17 @@ implements java.io.Serializable } //-- java.lang.Object getAccessionId() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'source'. * * @return Object @@ -198,6 +221,16 @@ implements java.io.Serializable } //-- void setAccessionId(java.lang.Object) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'source'. * * @param source the value of field 'source'. diff --git a/src/org/vamsas/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java index 25833ad..fbf02dd 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -162,6 +162,40 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript { //-- local scope } 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DbRef target = (DbRef) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DbRef target = (DbRef) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors } //-- org.vamsas.objects.core.DbRefDescriptor() diff --git a/src/org/vamsas/objects/core/Dendro.java b/src/org/vamsas/objects/core/Dendro.java new file mode 100644 index 0000000..eb04f13 --- /dev/null +++ b/src/org/vamsas/objects/core/Dendro.java @@ -0,0 +1,141 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; + +/** + * Class Dendro. + * + * @version $Revision$ $Date$ + */ +public class Dendro extends TreeType +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Dendro() + { + super(); + } //-- org.vamsas.objects.core.Dendro() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Note: hashCode() has not been overriden + * + * @param obj + * @return boolean + */ + public boolean equals(java.lang.Object obj) + { + if ( this == obj ) + return true; + + if (super.equals(obj)==false) + return false; + + if (obj instanceof Dendro) { + + Dendro temp = (Dendro)obj; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Method isValid + * + * + * + * @return boolean + */ + public boolean isValid() + { + try { + validate(); + } + catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } //-- boolean isValid() + + /** + * Method marshal + * + * + * + * @param out + */ + public void marshal(java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, out); + } //-- void marshal(java.io.Writer) + + /** + * Method marshal + * + * + * + * @param handler + */ + public void marshal(org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, handler); + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Dendro + */ + public static org.vamsas.objects.core.Dendro unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.objects.core.Dendro) Unmarshaller.unmarshal(org.vamsas.objects.core.Dendro.class, reader); + } //-- org.vamsas.objects.core.Dendro unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/org/vamsas/objects/core/DendroDescriptor.java b/src/org/vamsas/objects/core/DendroDescriptor.java new file mode 100644 index 0000000..1b3cc2f --- /dev/null +++ b/src/org/vamsas/objects/core/DendroDescriptor.java @@ -0,0 +1,167 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.mapping.AccessMode; +import org.exolab.castor.xml.TypeValidator; +import org.exolab.castor.xml.XMLFieldDescriptor; +import org.exolab.castor.xml.validators.*; + +/** + * Class DendroDescriptor. + * + * @version $Revision$ $Date$ + */ +public class DendroDescriptor extends TreeTypeDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field nsPrefix + */ + private java.lang.String nsPrefix; + + /** + * Field nsURI + */ + private java.lang.String nsURI; + + /** + * Field xmlName + */ + private java.lang.String xmlName; + + /** + * Field identity + */ + private org.exolab.castor.xml.XMLFieldDescriptor identity; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DendroDescriptor() + { + super(); + setExtendsWithoutFlatten(new TreeTypeDescriptor()); + nsURI = "http://www.vamsas.org"; + xmlName = "Dendro"; + } //-- org.vamsas.objects.core.DendroDescriptor() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode + * + * + * + * @return AccessMode + */ + public org.exolab.castor.mapping.AccessMode getAccessMode() + { + return null; + } //-- org.exolab.castor.mapping.AccessMode getAccessMode() + + /** + * Method getExtends + * + * + * + * @return ClassDescriptor + */ + public org.exolab.castor.mapping.ClassDescriptor getExtends() + { + return super.getExtends(); + } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() + + /** + * Method getIdentity + * + * + * + * @return FieldDescriptor + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity() + { + if (identity == null) + return super.getIdentity(); + return identity; + } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() + + /** + * Method getJavaClass + * + * + * + * @return Class + */ + public java.lang.Class getJavaClass() + { + return org.vamsas.objects.core.Dendro.class; + } //-- java.lang.Class getJavaClass() + + /** + * Method getNameSpacePrefix + * + * + * + * @return String + */ + public java.lang.String getNameSpacePrefix() + { + return nsPrefix; + } //-- java.lang.String getNameSpacePrefix() + + /** + * Method getNameSpaceURI + * + * + * + * @return String + */ + public java.lang.String getNameSpaceURI() + { + return nsURI; + } //-- java.lang.String getNameSpaceURI() + + /** + * Method getValidator + * + * + * + * @return TypeValidator + */ + public org.exolab.castor.xml.TypeValidator getValidator() + { + return this; + } //-- org.exolab.castor.xml.TypeValidator getValidator() + + /** + * Method getXMLName + * + * + * + * @return String + */ + public java.lang.String getXMLName() + { + return xmlName; + } //-- java.lang.String getXMLName() + +} diff --git a/src/org/vamsas/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java index bfea18e..95dd1fb 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -36,6 +36,11 @@ implements java.io.Serializable //--------------------------/ /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _user */ private java.lang.String _user; @@ -82,6 +87,13 @@ implements java.io.Serializable if (obj instanceof Entry) { Entry temp = (Entry)obj; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._user != null) { if (temp._user == null) return false; else if (!(this._user.equals(temp._user))) @@ -131,6 +143,17 @@ implements java.io.Serializable } //-- org.exolab.castor.types.Date getDate() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'user'. * * @return String @@ -208,6 +231,16 @@ implements java.io.Serializable } //-- void setDate(org.exolab.castor.types.Date) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'user'. * * @param user the value of field 'user'. diff --git a/src/org/vamsas/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java index e9651fb..718b4be 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -66,6 +66,40 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Entry target = (Entry) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Entry target = (Entry) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _user diff --git a/src/org/vamsas/objects/core/LockFile.java b/src/org/vamsas/objects/core/LockFile.java index 0d59af3..ef6fc07 100644 --- a/src/org/vamsas/objects/core/LockFile.java +++ b/src/org/vamsas/objects/core/LockFile.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/LockFileDescriptor.java b/src/org/vamsas/objects/core/LockFileDescriptor.java index 804521f..faf0570 100644 --- a/src/org/vamsas/objects/core/LockFileDescriptor.java +++ b/src/org/vamsas/objects/core/LockFileDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java index ed09008..9f0adc5 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java index 50225b3..71db58f 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/ProvenanceItem.java b/src/org/vamsas/objects/core/ProvenanceItem.java index 390895d..692b53b 100644 --- a/src/org/vamsas/objects/core/ProvenanceItem.java +++ b/src/org/vamsas/objects/core/ProvenanceItem.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java b/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java index 5dbca13..9bb7343 100644 --- a/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java +++ b/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ diff --git a/src/org/vamsas/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java index e24fcca..5988d65 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -40,11 +40,6 @@ implements java.io.Serializable */ private java.lang.String _dictionary; - /** - * Field _id - */ - private java.lang.String _id; - //----------------/ //- Constructors -/ @@ -84,13 +79,6 @@ implements java.io.Serializable } else if (temp._dictionary != null) return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; return true; } return false; @@ -108,17 +96,6 @@ implements java.io.Serializable } //-- java.lang.String getDictionary() /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** * Method isValid * * @@ -175,16 +152,6 @@ implements java.io.Serializable } //-- void setDictionary(java.lang.String) /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** * Method unmarshal * * diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java index c515dce..202b67f 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -101,42 +101,6 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc 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() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); //-- initialize element descriptors } //-- org.vamsas.objects.core.SequenceDescriptor() diff --git a/src/org/vamsas/objects/core/SequenceSet.java b/src/org/vamsas/objects/core/SequenceSet.java index 1402e02..f41fdc0 100644 --- a/src/org/vamsas/objects/core/SequenceSet.java +++ b/src/org/vamsas/objects/core/SequenceSet.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -53,6 +53,11 @@ implements java.io.Serializable private boolean _has_aligned; /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _sequenceList */ private java.util.Vector _sequenceList; @@ -249,6 +254,13 @@ implements java.io.Serializable return false; if (this._has_aligned != temp._has_aligned) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._sequenceList != null) { if (temp._sequenceList == null) return false; else if (!(this._sequenceList.equals(temp._sequenceList))) @@ -360,6 +372,17 @@ implements java.io.Serializable } //-- java.lang.String getGapChar() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'provenance'. * * @return Provenance @@ -663,6 +686,16 @@ implements java.io.Serializable } //-- void setGapChar(java.lang.String) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'provenance'. * * @param provenance the value of field 'provenance'. diff --git a/src/org/vamsas/objects/core/SequenceSetAnnotations.java b/src/org/vamsas/objects/core/SequenceSetAnnotations.java index 092dbba..347636c 100644 --- a/src/org/vamsas/objects/core/SequenceSetAnnotations.java +++ b/src/org/vamsas/objects/core/SequenceSetAnnotations.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -58,6 +58,11 @@ implements java.io.Serializable private java.lang.Object _seqRef; /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _description */ private java.lang.String _description; @@ -177,6 +182,13 @@ implements java.io.Serializable } else if (temp._seqRef != null) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._description != null) { if (temp._description == null) return false; else if (!(this._description.equals(temp._description))) @@ -292,6 +304,17 @@ implements java.io.Serializable } //-- java.lang.String getEnd() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'provenance'. * * @return Provenance @@ -470,6 +493,16 @@ implements java.io.Serializable } //-- void setEnd(java.lang.String) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'provenance'. * * @param provenance the value of field 'provenance'. diff --git a/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java index f648ed4..c270df7 100644 --- a/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -219,6 +219,40 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util { //-- local scope } 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _description diff --git a/src/org/vamsas/objects/core/SequenceSetDescriptor.java b/src/org/vamsas/objects/core/SequenceSetDescriptor.java index f6d090e..0f05d2a 100644 --- a/src/org/vamsas/objects/core/SequenceSetDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceSetDescriptor.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -147,6 +147,40 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _sequenceList diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java index 4c16ba3..e6204d6 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -58,6 +58,11 @@ implements java.io.Serializable private boolean _has_end; /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _sequence */ private java.lang.String _sequence; @@ -170,6 +175,13 @@ implements java.io.Serializable return false; if (this._has_end != temp._has_end) return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._sequence != null) { if (temp._sequence == null) return false; else if (!(this._sequence.equals(temp._sequence))) @@ -256,6 +268,17 @@ implements java.io.Serializable } //-- int getEnd() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'name'. * * @return String @@ -428,6 +451,16 @@ implements java.io.Serializable } //-- void setEnd(int) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'name'. * * @param name the value of field 'name'. diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java index be52f24..3740da3 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -150,6 +150,40 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _sequence diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java index 7687cbb..8290635 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -26,26 +26,11 @@ import org.xml.sax.ContentHandler; * * @version $Revision$ $Date$ */ -public class Tree extends org.vamsas.client.object +public class Tree extends TreeType implements java.io.Serializable { - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - /** - * Field _newickFormat - */ - private java.lang.String _newickFormat; - - //----------------/ //- Constructors -/ //----------------/ @@ -77,48 +62,12 @@ implements java.io.Serializable if (obj instanceof Tree) { Tree temp = (Tree)obj; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - if (this._newickFormat != null) { - if (temp._newickFormat == null) return false; - else if (!(this._newickFormat.equals(temp._newickFormat))) - return false; - } - else if (temp._newickFormat != null) - return false; return true; } return false; } //-- boolean equals(java.lang.Object) /** - * Returns the value of field 'newickFormat'. - * - * @return String - * @return the value of field 'newickFormat'. - */ - public java.lang.String getNewickFormat() - { - return this._newickFormat; - } //-- java.lang.String getNewickFormat() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** * Method isValid * * @@ -165,26 +114,6 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** - * Sets the value of field 'newickFormat'. - * - * @param newickFormat the value of field 'newickFormat'. - */ - public void setNewickFormat(java.lang.String newickFormat) - { - this._newickFormat = newickFormat; - } //-- void setNewickFormat(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** * Method unmarshal * * diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java index 0918e4e..b0012ef 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -21,7 +21,7 @@ import org.exolab.castor.xml.validators.*; * * @version $Revision$ $Date$ */ -public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { +public class TreeDescriptor extends TreeTypeDescriptor { //--------------------------/ @@ -56,94 +56,9 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto public TreeDescriptor() { super(); + setExtendsWithoutFlatten(new TreeTypeDescriptor()); nsURI = "http://www.vamsas.org"; xmlName = "tree"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _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() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - 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); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _newickFormat - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormat", "newickFormat", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewickFormat(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setNewickFormat( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _newickFormat - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); } //-- org.vamsas.objects.core.TreeDescriptor() @@ -172,7 +87,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto */ public org.exolab.castor.mapping.ClassDescriptor getExtends() { - return null; + return super.getExtends(); } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() /** @@ -184,6 +99,8 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto */ public org.exolab.castor.mapping.FieldDescriptor getIdentity() { + if (identity == null) + return super.getIdentity(); return identity; } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() diff --git a/src/org/vamsas/objects/core/TreeType.java b/src/org/vamsas/objects/core/TreeType.java new file mode 100644 index 0000000..9cb6dca --- /dev/null +++ b/src/org/vamsas/objects/core/TreeType.java @@ -0,0 +1,372 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +import java.util.Enumeration; +import java.util.Vector; +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; + +/** + * Class TreeType. + * + * @version $Revision$ $Date$ + */ +public class TreeType extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id + */ + private java.lang.String _id; + + /** + * Field _newickFormatList + */ + private java.util.Vector _newickFormatList; + + /** + * Field _provenance + */ + private org.vamsas.objects.core.Provenance _provenance; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public TreeType() + { + super(); + _newickFormatList = new Vector(); + } //-- org.vamsas.objects.core.TreeType() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addNewickFormat + * + * + * + * @param vNewickFormat + */ + public void addNewickFormat(java.lang.String vNewickFormat) + throws java.lang.IndexOutOfBoundsException + { + _newickFormatList.addElement(vNewickFormat); + } //-- void addNewickFormat(java.lang.String) + + /** + * Method addNewickFormat + * + * + * + * @param index + * @param vNewickFormat + */ + public void addNewickFormat(int index, java.lang.String vNewickFormat) + throws java.lang.IndexOutOfBoundsException + { + _newickFormatList.insertElementAt(vNewickFormat, index); + } //-- void addNewickFormat(int, java.lang.String) + + /** + * Method enumerateNewickFormat + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateNewickFormat() + { + return _newickFormatList.elements(); + } //-- java.util.Enumeration enumerateNewickFormat() + + /** + * Note: hashCode() has not been overriden + * + * @param obj + * @return boolean + */ + public boolean equals(java.lang.Object obj) + { + if ( this == obj ) + return true; + + if (super.equals(obj)==false) + return false; + + if (obj instanceof TreeType) { + + TreeType temp = (TreeType)obj; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; + if (this._newickFormatList != null) { + if (temp._newickFormatList == null) return false; + else if (!(this._newickFormatList.equals(temp._newickFormatList))) + return false; + } + else if (temp._newickFormatList != null) + return false; + if (this._provenance != null) { + if (temp._provenance == null) return false; + else if (!(this._provenance.equals(temp._provenance))) + return false; + } + else if (temp._provenance != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** + * Method getNewickFormat + * + * + * + * @param index + * @return String + */ + public java.lang.String getNewickFormat(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _newickFormatList.size())) { + throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]"); + } + + return (String)_newickFormatList.elementAt(index); + } //-- java.lang.String getNewickFormat(int) + + /** + * Method getNewickFormat + * + * + * + * @return String + */ + public java.lang.String[] getNewickFormat() + { + int size = _newickFormatList.size(); + java.lang.String[] mArray = new java.lang.String[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (String)_newickFormatList.elementAt(index); + } + return mArray; + } //-- java.lang.String[] getNewickFormat() + + /** + * Method getNewickFormatCount + * + * + * + * @return int + */ + public int getNewickFormatCount() + { + return _newickFormatList.size(); + } //-- int getNewickFormatCount() + + /** + * Returns the value of field 'provenance'. + * + * @return Provenance + * @return the value of field 'provenance'. + */ + public org.vamsas.objects.core.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.objects.core.Provenance getProvenance() + + /** + * Method isValid + * + * + * + * @return boolean + */ + public boolean isValid() + { + try { + validate(); + } + catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } //-- boolean isValid() + + /** + * Method marshal + * + * + * + * @param out + */ + public void marshal(java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, out); + } //-- void marshal(java.io.Writer) + + /** + * Method marshal + * + * + * + * @param handler + */ + public void marshal(org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, handler); + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Method removeAllNewickFormat + * + */ + public void removeAllNewickFormat() + { + _newickFormatList.removeAllElements(); + } //-- void removeAllNewickFormat() + + /** + * Method removeNewickFormat + * + * + * + * @param index + * @return String + */ + public java.lang.String removeNewickFormat(int index) + { + java.lang.Object obj = _newickFormatList.elementAt(index); + _newickFormatList.removeElementAt(index); + return (String)obj; + } //-- java.lang.String removeNewickFormat(int) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** + * Method setNewickFormat + * + * + * + * @param index + * @param vNewickFormat + */ + public void setNewickFormat(int index, java.lang.String vNewickFormat) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _newickFormatList.size())) { + throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]"); + } + _newickFormatList.setElementAt(vNewickFormat, index); + } //-- void setNewickFormat(int, java.lang.String) + + /** + * Method setNewickFormat + * + * + * + * @param newickFormatArray + */ + public void setNewickFormat(java.lang.String[] newickFormatArray) + { + //-- copy array + _newickFormatList.removeAllElements(); + for (int i = 0; i < newickFormatArray.length; i++) { + _newickFormatList.addElement(newickFormatArray[i]); + } + } //-- void setNewickFormat(java.lang.String) + + /** + * Sets the value of field 'provenance'. + * + * @param provenance the value of field 'provenance'. + */ + public void setProvenance(org.vamsas.objects.core.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.objects.core.Provenance) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return TreeType + */ + public static org.vamsas.objects.core.TreeType unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.objects.core.TreeType) Unmarshaller.unmarshal(org.vamsas.objects.core.TreeType.class, reader); + } //-- org.vamsas.objects.core.TreeType unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/org/vamsas/objects/core/TreeTypeDescriptor.java b/src/org/vamsas/objects/core/TreeTypeDescriptor.java new file mode 100644 index 0000000..7641bc8 --- /dev/null +++ b/src/org/vamsas/objects/core/TreeTypeDescriptor.java @@ -0,0 +1,284 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.mapping.AccessMode; +import org.exolab.castor.xml.TypeValidator; +import org.exolab.castor.xml.XMLFieldDescriptor; +import org.exolab.castor.xml.validators.*; + +/** + * Class TreeTypeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class TreeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field nsPrefix + */ + private java.lang.String nsPrefix; + + /** + * Field nsURI + */ + private java.lang.String nsURI; + + /** + * Field xmlName + */ + private java.lang.String xmlName; + + /** + * Field identity + */ + private org.exolab.castor.xml.XMLFieldDescriptor identity; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public TreeTypeDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "TreeType"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + TreeType target = (TreeType) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + TreeType target = (TreeType) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _newickFormatList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + TreeType target = (TreeType) object; + return target.getNewickFormat(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + TreeType target = (TreeType) object; + target.addNewickFormat( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _newickFormatList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + TreeType target = (TreeType) object; + return target.getProvenance(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + TreeType target = (TreeType) object; + target.setProvenance( (org.vamsas.objects.core.Provenance) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + 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); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _provenance + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.objects.core.TreeTypeDescriptor() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode + * + * + * + * @return AccessMode + */ + public org.exolab.castor.mapping.AccessMode getAccessMode() + { + return null; + } //-- org.exolab.castor.mapping.AccessMode getAccessMode() + + /** + * Method getExtends + * + * + * + * @return ClassDescriptor + */ + public org.exolab.castor.mapping.ClassDescriptor getExtends() + { + return null; + } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() + + /** + * Method getIdentity + * + * + * + * @return FieldDescriptor + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity() + { + return identity; + } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() + + /** + * Method getJavaClass + * + * + * + * @return Class + */ + public java.lang.Class getJavaClass() + { + return org.vamsas.objects.core.TreeType.class; + } //-- java.lang.Class getJavaClass() + + /** + * Method getNameSpacePrefix + * + * + * + * @return String + */ + public java.lang.String getNameSpacePrefix() + { + return nsPrefix; + } //-- java.lang.String getNameSpacePrefix() + + /** + * Method getNameSpaceURI + * + * + * + * @return String + */ + public java.lang.String getNameSpaceURI() + { + return nsURI; + } //-- java.lang.String getNameSpaceURI() + + /** + * Method getValidator + * + * + * + * @return TypeValidator + */ + public org.exolab.castor.xml.TypeValidator getValidator() + { + return this; + } //-- org.exolab.castor.xml.TypeValidator getValidator() + + /** + * Method getXMLName + * + * + * + * @return String + */ + public java.lang.String getXMLName() + { + return xmlName; + } //-- java.lang.String getXMLName() + +} diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java index c1d4fa5..12a81f2 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -38,9 +38,14 @@ implements java.io.Serializable //--------------------------/ /** - * Field _treeList + * Field _id */ - private java.util.Vector _treeList; + private java.lang.String _id; + + /** + * Field _dendroList + */ + private java.util.Vector _dendroList; /** * Field _sequenceSetList @@ -55,7 +60,7 @@ implements java.io.Serializable public VAMSAS() { super(); - _treeList = new Vector(); + _dendroList = new Vector(); _sequenceSetList = new Vector(); } //-- org.vamsas.objects.core.VAMSAS() @@ -65,82 +70,82 @@ implements java.io.Serializable //-----------/ /** - * Method addSequenceSet + * Method addDendro * * * - * @param vSequenceSet + * @param vDendro */ - public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet) + public void addDendro(org.vamsas.objects.core.Dendro vDendro) throws java.lang.IndexOutOfBoundsException { - _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) + _dendroList.addElement(vDendro); + } //-- void addDendro(org.vamsas.objects.core.Dendro) /** - * Method addSequenceSet + * Method addDendro * * * * @param index - * @param vSequenceSet + * @param vDendro */ - public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet) + public void addDendro(int index, org.vamsas.objects.core.Dendro vDendro) throws java.lang.IndexOutOfBoundsException { - _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) + _dendroList.insertElementAt(vDendro, index); + } //-- void addDendro(int, org.vamsas.objects.core.Dendro) /** - * Method addTree + * Method addSequenceSet * * * - * @param vTree + * @param vSequenceSet */ - public void addTree(java.lang.String vTree) + public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException { - _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) + _sequenceSetList.addElement(vSequenceSet); + } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) /** - * Method addTree + * Method addSequenceSet * * * * @param index - * @param vTree + * @param vSequenceSet */ - public void addTree(int index, java.lang.String vTree) + public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) + _sequenceSetList.insertElementAt(vSequenceSet, index); + } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) /** - * Method enumerateSequenceSet + * Method enumerateDendro * * * * @return Enumeration */ - public java.util.Enumeration enumerateSequenceSet() + public java.util.Enumeration enumerateDendro() { - return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() + return _dendroList.elements(); + } //-- java.util.Enumeration enumerateDendro() /** - * Method enumerateTree + * Method enumerateSequenceSet * * * * @return Enumeration */ - public java.util.Enumeration enumerateTree() + public java.util.Enumeration enumerateSequenceSet() { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() + return _sequenceSetList.elements(); + } //-- java.util.Enumeration enumerateSequenceSet() /** * Note: hashCode() has not been overriden @@ -159,12 +164,19 @@ implements java.io.Serializable if (obj instanceof VAMSAS) { VAMSAS temp = (VAMSAS)obj; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) return false; } - else if (temp._treeList != null) + else if (temp._id != null) + return false; + if (this._dendroList != null) { + if (temp._dendroList == null) return false; + else if (!(this._dendroList.equals(temp._dendroList))) + return false; + } + else if (temp._dendroList != null) return false; if (this._sequenceSetList != null) { if (temp._sequenceSetList == null) return false; @@ -179,100 +191,111 @@ implements java.io.Serializable } //-- boolean equals(java.lang.Object) /** - * Method getSequenceSet + * Method getDendro * * * * @param index - * @return SequenceSet + * @return Dendro */ - public org.vamsas.objects.core.SequenceSet getSequenceSet(int index) + public org.vamsas.objects.core.Dendro getDendro(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]"); + if ((index < 0) || (index > _dendroList.size())) { + throw new IndexOutOfBoundsException("getDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]"); } - return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index); - } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) + return (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index); + } //-- org.vamsas.objects.core.Dendro getDendro(int) /** - * Method getSequenceSet + * Method getDendro * * * - * @return SequenceSet + * @return Dendro */ - public org.vamsas.objects.core.SequenceSet[] getSequenceSet() + public org.vamsas.objects.core.Dendro[] getDendro() { - int size = _sequenceSetList.size(); - org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size]; + int size = _dendroList.size(); + org.vamsas.objects.core.Dendro[] mArray = new org.vamsas.objects.core.Dendro[size]; for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index); + mArray[index] = (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index); } return mArray; - } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() + } //-- org.vamsas.objects.core.Dendro[] getDendro() /** - * Method getSequenceSetCount + * Method getDendroCount * * * * @return int */ - public int getSequenceSetCount() + public int getDendroCount() { - return _sequenceSetList.size(); - } //-- int getSequenceSetCount() + return _dendroList.size(); + } //-- int getDendroCount() /** - * Method getTree + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** + * Method getSequenceSet * * * * @param index - * @return String + * @return SequenceSet */ - public java.lang.String getTree(int index) + public org.vamsas.objects.core.SequenceSet getSequenceSet(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); + if ((index < 0) || (index > _sequenceSetList.size())) { + throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]"); } - return (String)_treeList.elementAt(index); - } //-- java.lang.String getTree(int) + return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index); + } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) /** - * Method getTree + * Method getSequenceSet * * * - * @return String + * @return SequenceSet */ - public java.lang.String[] getTree() + public org.vamsas.objects.core.SequenceSet[] getSequenceSet() { - int size = _treeList.size(); - java.lang.String[] mArray = new java.lang.String[size]; + int size = _sequenceSetList.size(); + org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size]; for (int index = 0; index < size; index++) { - mArray[index] = (String)_treeList.elementAt(index); + mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index); } return mArray; - } //-- java.lang.String[] getTree() + } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() /** - * Method getTreeCount + * Method getSequenceSetCount * * * * @return int */ - public int getTreeCount() + public int getSequenceSetCount() { - return _treeList.size(); - } //-- int getTreeCount() + return _sequenceSetList.size(); + } //-- int getSequenceSetCount() /** * Method isValid @@ -321,6 +344,15 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** + * Method removeAllDendro + * + */ + public void removeAllDendro() + { + _dendroList.removeAllElements(); + } //-- void removeAllDendro() + + /** * Method removeAllSequenceSet * */ @@ -330,13 +362,19 @@ implements java.io.Serializable } //-- void removeAllSequenceSet() /** - * Method removeAllTree + * Method removeDendro + * * + * + * @param index + * @return Dendro */ - public void removeAllTree() + public org.vamsas.objects.core.Dendro removeDendro(int index) { - _treeList.removeAllElements(); - } //-- void removeAllTree() + java.lang.Object obj = _dendroList.elementAt(index); + _dendroList.removeElementAt(index); + return (org.vamsas.objects.core.Dendro) obj; + } //-- org.vamsas.objects.core.Dendro removeDendro(int) /** * Method removeSequenceSet @@ -354,19 +392,48 @@ implements java.io.Serializable } //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int) /** - * Method removeTree + * Method setDendro * * * * @param index - * @return String + * @param vDendro + */ + public void setDendro(int index, org.vamsas.objects.core.Dendro vDendro) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _dendroList.size())) { + throw new IndexOutOfBoundsException("setDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]"); + } + _dendroList.setElementAt(vDendro, index); + } //-- void setDendro(int, org.vamsas.objects.core.Dendro) + + /** + * Method setDendro + * + * + * + * @param dendroArray + */ + public void setDendro(org.vamsas.objects.core.Dendro[] dendroArray) + { + //-- copy array + _dendroList.removeAllElements(); + for (int i = 0; i < dendroArray.length; i++) { + _dendroList.addElement(dendroArray[i]); + } + } //-- void setDendro(org.vamsas.objects.core.Dendro) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. */ - public java.lang.String removeTree(int index) + public void setId(java.lang.String id) { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (String)obj; - } //-- java.lang.String removeTree(int) + this._id = id; + } //-- void setId(java.lang.String) /** * Method setSequenceSet @@ -403,40 +470,6 @@ implements java.io.Serializable } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet) /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(java.lang.String[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(java.lang.String) - - /** * Method unmarshal * * diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java index a01bd55..e46ddd0 100644 --- 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 0.9.9M1, using an XML + * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ @@ -66,31 +66,64 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip 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() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); + //-- _dendroList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Dendro.class, "_dendroList", "Dendro", org.exolab.castor.xml.NodeType.Element); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { VAMSAS target = (VAMSAS) object; - return target.getTree(); + return target.getDendro(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { VAMSAS target = (VAMSAS) object; - target.addTree( (java.lang.String) value); + target.addDendro( (org.vamsas.objects.core.Dendro) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } } public java.lang.Object newInstance( java.lang.Object parent ) { - return null; + return new org.vamsas.objects.core.Dendro(); } }; desc.setHandler(handler); @@ -98,13 +131,10 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip desc.setMultivalued(true); addFieldDescriptor(desc); - //-- validation code for: _treeList + //-- validation code for: _dendroList fieldValidator = new org.exolab.castor.xml.FieldValidator(); fieldValidator.setMinOccurs(0); { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); //-- _sequenceSetList diff --git a/tools/castor-0.9.9M1-srcgen-ant-task.jar b/tools/castor-0.9.9M2-srcgen-ant-task.jar similarity index 61% rename from tools/castor-0.9.9M1-srcgen-ant-task.jar rename to tools/castor-0.9.9M2-srcgen-ant-task.jar index 3f860b6..63672e6 100644 Binary files a/tools/castor-0.9.9M1-srcgen-ant-task.jar and b/tools/castor-0.9.9M2-srcgen-ant-task.jar differ