From 186fbddd0b47f51398042705264723712e77a5e2 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 19 Sep 2005 13:20:36 +0000 Subject: [PATCH 1/1] first attempt at object build. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@17 be28352e-c001-0410-b1a7-c7978e42abec --- schemas/castorbuilder.properties | 63 ++ src/org/vamsas/client/objects/Alignment.java | 618 +++++++++++++ .../client/objects/AlignmentAnnotations.java | 506 +++++++++++ .../objects/AlignmentAnnotationsDescriptor.java | 368 ++++++++ .../vamsas/client/objects/AlignmentDescriptor.java | 315 +++++++ .../vamsas/client/objects/AlignmentSequence.java | 179 ++++ .../objects/AlignmentSequenceDescriptor.java | 210 +++++ .../vamsas/client/objects/AnnotationElement.java | 360 ++++++++ .../objects/AnnotationElementDescriptor.java | 380 ++++++++ src/org/vamsas/client/objects/Application.java | 212 +++++ src/org/vamsas/client/objects/ApplicationData.java | 179 ++++ .../client/objects/ApplicationDataDescriptor.java | 210 +++++ .../client/objects/ApplicationDescriptor.java | 237 +++++ src/org/vamsas/client/objects/DbRef.java | 245 ++++++ src/org/vamsas/client/objects/DbRefDescriptor.java | 270 ++++++ src/org/vamsas/client/objects/Entry.java | 245 ++++++ src/org/vamsas/client/objects/EntryDescriptor.java | 292 +++++++ src/org/vamsas/client/objects/LockFile.java | 182 ++++ .../vamsas/client/objects/LockFileDescriptor.java | 207 +++++ src/org/vamsas/client/objects/Provenance.java | 350 ++++++++ .../client/objects/ProvenanceDescriptor.java | 206 +++++ src/org/vamsas/client/objects/ProvenanceItem.java | 71 ++ .../client/objects/ProvenanceItemDescriptor.java | 210 +++++ src/org/vamsas/client/objects/Sequence.java | 212 +++++ .../vamsas/client/objects/SequenceDescriptor.java | 247 ++++++ src/org/vamsas/client/objects/SequenceSet.java | 908 ++++++++++++++++++++ .../client/objects/SequenceSetAnnotations.java | 581 +++++++++++++ .../objects/SequenceSetAnnotationsDescriptor.java | 474 ++++++++++ .../client/objects/SequenceSetDescriptor.java | 433 ++++++++++ src/org/vamsas/client/objects/SequenceType.java | 529 ++++++++++++ .../client/objects/SequenceTypeDescriptor.java | 373 ++++++++ src/org/vamsas/client/objects/Tree.java | 212 +++++ src/org/vamsas/client/objects/TreeDescriptor.java | 250 ++++++ src/org/vamsas/client/objects/VAMSAS.java | 550 ++++++++++++ .../vamsas/client/objects/VAMSASDescriptor.java | 248 ++++++ 35 files changed, 11132 insertions(+) create mode 100644 schemas/castorbuilder.properties create mode 100644 schemas/vamsas15_9.mapping create mode 100644 src/org/vamsas/client/objects/Alignment.java create mode 100644 src/org/vamsas/client/objects/AlignmentAnnotations.java create mode 100644 src/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java create mode 100644 src/org/vamsas/client/objects/AlignmentDescriptor.java create mode 100644 src/org/vamsas/client/objects/AlignmentSequence.java create mode 100644 src/org/vamsas/client/objects/AlignmentSequenceDescriptor.java create mode 100644 src/org/vamsas/client/objects/AnnotationElement.java create mode 100644 src/org/vamsas/client/objects/AnnotationElementDescriptor.java create mode 100644 src/org/vamsas/client/objects/Application.java create mode 100644 src/org/vamsas/client/objects/ApplicationData.java create mode 100644 src/org/vamsas/client/objects/ApplicationDataDescriptor.java create mode 100644 src/org/vamsas/client/objects/ApplicationDescriptor.java create mode 100644 src/org/vamsas/client/objects/DbRef.java create mode 100644 src/org/vamsas/client/objects/DbRefDescriptor.java create mode 100644 src/org/vamsas/client/objects/Entry.java create mode 100644 src/org/vamsas/client/objects/EntryDescriptor.java create mode 100644 src/org/vamsas/client/objects/LockFile.java create mode 100644 src/org/vamsas/client/objects/LockFileDescriptor.java create mode 100644 src/org/vamsas/client/objects/Provenance.java create mode 100644 src/org/vamsas/client/objects/ProvenanceDescriptor.java create mode 100644 src/org/vamsas/client/objects/ProvenanceItem.java create mode 100644 src/org/vamsas/client/objects/ProvenanceItemDescriptor.java create mode 100644 src/org/vamsas/client/objects/Sequence.java create mode 100644 src/org/vamsas/client/objects/SequenceDescriptor.java create mode 100644 src/org/vamsas/client/objects/SequenceSet.java create mode 100644 src/org/vamsas/client/objects/SequenceSetAnnotations.java create mode 100644 src/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java create mode 100644 src/org/vamsas/client/objects/SequenceSetDescriptor.java create mode 100644 src/org/vamsas/client/objects/SequenceType.java create mode 100644 src/org/vamsas/client/objects/SequenceTypeDescriptor.java create mode 100644 src/org/vamsas/client/objects/Tree.java create mode 100644 src/org/vamsas/client/objects/TreeDescriptor.java create mode 100644 src/org/vamsas/client/objects/VAMSAS.java create mode 100644 src/org/vamsas/client/objects/VAMSASDescriptor.java diff --git a/schemas/castorbuilder.properties b/schemas/castorbuilder.properties new file mode 100644 index 0000000..d2f669e --- /dev/null +++ b/schemas/castorbuilder.properties @@ -0,0 +1,63 @@ +# +# Property file for SourceCodeGenerator +# +# $Id$ + +# To enable bound properties uncomment the following line. Please +# note that currently *all* fields will be treated as bound properties +# when enabled. This will change in the future when we introduce +# fine grained control over each class and it's properties. +# +#org.exolab.castor.builder.boundproperties=true + +# Java class mapping of 's and 's +# +#org.exolab.castor.builder.javaclassmapping=element + +# This property allows one to specify the super class of *all* +# generated classes +# +org.exolab.castor.builder.superclass=org.vamsas.client.object + +# XML namespace mapping to Java packages +# +#org.exolab.castor.builder.nspackages=\ + http://www.xyz.com/schemas/project=com.xyz.schemas.project,\ + http://www.xyz.com/schemas/person=com.xyz.schemas.person + +# Set to true if you want to generate the equals method +# for each generated class +# false by default +# +org.exolab.castor.builder.equalsmethod=true + +# Set to true if you want to use Object Wrappers instead +# of primitives (e.g Float instead of float). +# false by default. +# +#org.exolab.castor.builder.primitivetowrapper=false + +# Set to true if you want the generated class descriptors to +# expose the element and attribute names they contain. +# false by default. +# +#org.exolab.castor.builder.classdescfieldnames=false + +# Set to true if you want the generated source code to contain +# Extra methods for the collection fields, such as get/set using +# the collection type in addition to the type-safe array. +# Set this to true if you want your code to be more compatible +# with Castor JDO. This is false by default. +# +org.exolab.castor.builder.extraCollectionMethods=true + +# Use old-style (Castor 0.9.3.9) of naming that uppercases +# names after an underscore +# +#org.exolab.castor.xml.JavaNaming.upperCaseAfterUnderscore=true + +# This property specifies whether generated enumerated type +# classes implement the EnumeratedTypeAccess interface. +# false by default +#org.exolab.castor.builder.enumTypeAccessInterface=true + diff --git a/schemas/vamsas15_9.mapping b/schemas/vamsas15_9.mapping new file mode 100644 index 0000000..e69de29 diff --git a/src/org/vamsas/client/objects/Alignment.java b/src/org/vamsas/client/objects/Alignment.java new file mode 100644 index 0000000..31413a3 --- /dev/null +++ b/src/org/vamsas/client/objects/Alignment.java @@ -0,0 +1,618 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Alignment. + * + * @version $Revision$ $Date$ + */ +public class Alignment extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _alignmentAnnotations + */ + private org.vamsas.client.objects.AlignmentAnnotations _alignmentAnnotations; + + /** + * Field _treeList + */ + private java.util.Vector _treeList; + + /** + * Field _alignmentSequenceList + */ + private java.util.Vector _alignmentSequenceList; + + /** + * Field _provenance + */ + private org.vamsas.client.objects.Provenance _provenance; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Alignment() + { + super(); + _treeList = new Vector(); + _alignmentSequenceList = new Vector(); + } //-- org.vamsas.client.objects.Alignment() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAlignmentSequence + * + * + * + * @param vAlignmentSequence + */ + public void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) + throws java.lang.IndexOutOfBoundsException + { + _alignmentSequenceList.addElement(vAlignmentSequence); + } //-- void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence) + + /** + * Method addAlignmentSequence + * + * + * + * @param index + * @param vAlignmentSequence + */ + public void addAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) + throws java.lang.IndexOutOfBoundsException + { + _alignmentSequenceList.insertElementAt(vAlignmentSequence, index); + } //-- void addAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence) + + /** + * Method addTree + * + * + * + * @param vTree + */ + public void addTree(org.vamsas.client.objects.Tree vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.addElement(vTree); + } //-- void addTree(org.vamsas.client.objects.Tree) + + /** + * Method addTree + * + * + * + * @param index + * @param vTree + */ + public void addTree(int index, org.vamsas.client.objects.Tree vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.insertElementAt(vTree, index); + } //-- void addTree(int, org.vamsas.client.objects.Tree) + + /** + * Method enumerateAlignmentSequence + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAlignmentSequence() + { + return _alignmentSequenceList.elements(); + } //-- java.util.Enumeration enumerateAlignmentSequence() + + /** + * Method enumerateTree + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateTree() + { + return _treeList.elements(); + } //-- java.util.Enumeration enumerateTree() + + /** + * 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 Alignment) { + + Alignment temp = (Alignment)obj; + if (this._alignmentAnnotations != null) { + if (temp._alignmentAnnotations == null) return false; + else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations))) + return false; + } + else if (temp._alignmentAnnotations != null) + return false; + if (this._treeList != null) { + if (temp._treeList == null) return false; + else if (!(this._treeList.equals(temp._treeList))) + return false; + } + else if (temp._treeList != null) + return false; + if (this._alignmentSequenceList != null) { + if (temp._alignmentSequenceList == null) return false; + else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList))) + return false; + } + else if (temp._alignmentSequenceList != 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 'alignmentAnnotations'. + * + * @return AlignmentAnnotations + * @return the value of field 'alignmentAnnotations'. + */ + public org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations() + { + return this._alignmentAnnotations; + } //-- org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations() + + /** + * Method getAlignmentSequence + * + * + * + * @param index + * @return AlignmentSequence + */ + public org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentSequenceList.size())) { + throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); + } + + return (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index); + } //-- org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int) + + /** + * Method getAlignmentSequence + * + * + * + * @return AlignmentSequence + */ + public org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence() + { + int size = _alignmentSequenceList.size(); + org.vamsas.client.objects.AlignmentSequence[] mArray = new org.vamsas.client.objects.AlignmentSequence[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence() + + /** + * Method getAlignmentSequenceAsReference + * + * Returns a reference to 'alignmentSequence'. No type checking + * is performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getAlignmentSequenceAsReference() + { + return _alignmentSequenceList; + } //-- java.util.Vector getAlignmentSequenceAsReference() + + /** + * Method getAlignmentSequenceCount + * + * + * + * @return int + */ + public int getAlignmentSequenceCount() + { + return _alignmentSequenceList.size(); + } //-- int getAlignmentSequenceCount() + + /** + * Returns the value of field 'provenance'. + * + * @return Provenance + * @return the value of field 'provenance'. + */ + public org.vamsas.client.objects.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.client.objects.Provenance getProvenance() + + /** + * Method getTree + * + * + * + * @param index + * @return Tree + */ + public org.vamsas.client.objects.Tree getTree(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()+ "]"); + } + + return (org.vamsas.client.objects.Tree) _treeList.elementAt(index); + } //-- org.vamsas.client.objects.Tree getTree(int) + + /** + * Method getTree + * + * + * + * @return Tree + */ + public org.vamsas.client.objects.Tree[] getTree() + { + int size = _treeList.size(); + org.vamsas.client.objects.Tree[] mArray = new org.vamsas.client.objects.Tree[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.Tree) _treeList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.Tree[] getTree() + + /** + * Method getTreeAsReference + * + * Returns a reference to 'tree'. No type checking is performed + * on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getTreeAsReference() + { + return _treeList; + } //-- java.util.Vector getTreeAsReference() + + /** + * Method getTreeCount + * + * + * + * @return int + */ + public int getTreeCount() + { + return _treeList.size(); + } //-- int getTreeCount() + + /** + * 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 removeAlignmentSequence + * + * + * + * @param index + * @return AlignmentSequence + */ + public org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int index) + { + java.lang.Object obj = _alignmentSequenceList.elementAt(index); + _alignmentSequenceList.removeElementAt(index); + return (org.vamsas.client.objects.AlignmentSequence) obj; + } //-- org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int) + + /** + * Method removeAllAlignmentSequence + * + */ + public void removeAllAlignmentSequence() + { + _alignmentSequenceList.removeAllElements(); + } //-- void removeAllAlignmentSequence() + + /** + * Method removeAllTree + * + */ + public void removeAllTree() + { + _treeList.removeAllElements(); + } //-- void removeAllTree() + + /** + * Method removeTree + * + * + * + * @param index + * @return Tree + */ + public org.vamsas.client.objects.Tree removeTree(int index) + { + java.lang.Object obj = _treeList.elementAt(index); + _treeList.removeElementAt(index); + return (org.vamsas.client.objects.Tree) obj; + } //-- org.vamsas.client.objects.Tree removeTree(int) + + /** + * Sets the value of field 'alignmentAnnotations'. + * + * @param alignmentAnnotations the value of field + * 'alignmentAnnotations'. + */ + public void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations alignmentAnnotations) + { + this._alignmentAnnotations = alignmentAnnotations; + } //-- void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations) + + /** + * Method setAlignmentSequence + * + * + * + * @param index + * @param vAlignmentSequence + */ + public void setAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentSequenceList.size())) { + throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); + } + _alignmentSequenceList.setElementAt(vAlignmentSequence, index); + } //-- void setAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence) + + /** + * Method setAlignmentSequence + * + * + * + * @param alignmentSequenceArray + */ + public void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence[] alignmentSequenceArray) + { + //-- copy array + _alignmentSequenceList.removeAllElements(); + for (int i = 0; i < alignmentSequenceArray.length; i++) { + _alignmentSequenceList.addElement(alignmentSequenceArray[i]); + } + } //-- void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence) + + /** + * Method setAlignmentSequence + * + * Sets the value of 'alignmentSequence' by copying the given + * Vector. + * + * @param alignmentSequenceVector the Vector to copy. + */ + public void setAlignmentSequence(java.util.Vector alignmentSequenceVector) + { + //-- copy vector + _alignmentSequenceList.removeAllElements(); + for (int i = 0; i < alignmentSequenceVector.size(); i++) { + _alignmentSequenceList.addElement((org.vamsas.client.objects.AlignmentSequence)alignmentSequenceVector.elementAt(i)); + } + } //-- void setAlignmentSequence(java.util.Vector) + + /** + * Method setAlignmentSequenceAsReference + * + * Sets the value of 'alignmentSequence' by setting it to the + * given Vector. No type checking is performed. + * + * @param alignmentSequenceVector the Vector to copy. + */ + public void setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector) + { + _alignmentSequenceList = alignmentSequenceVector; + } //-- void setAlignmentSequenceAsReference(java.util.Vector) + + /** + * Sets the value of field 'provenance'. + * + * @param provenance the value of field 'provenance'. + */ + public void setProvenance(org.vamsas.client.objects.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.client.objects.Provenance) + + /** + * Method setTree + * + * + * + * @param index + * @param vTree + */ + public void setTree(int index, org.vamsas.client.objects.Tree 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, org.vamsas.client.objects.Tree) + + /** + * Method setTree + * + * + * + * @param treeArray + */ + public void setTree(org.vamsas.client.objects.Tree[] treeArray) + { + //-- copy array + _treeList.removeAllElements(); + for (int i = 0; i < treeArray.length; i++) { + _treeList.addElement(treeArray[i]); + } + } //-- void setTree(org.vamsas.client.objects.Tree) + + /** + * Method setTree + * + * Sets the value of 'tree' by copying the given Vector. + * + * @param treeVector the Vector to copy. + */ + public void setTree(java.util.Vector treeVector) + { + //-- copy vector + _treeList.removeAllElements(); + for (int i = 0; i < treeVector.size(); i++) { + _treeList.addElement((org.vamsas.client.objects.Tree)treeVector.elementAt(i)); + } + } //-- void setTree(java.util.Vector) + + /** + * Method setTreeAsReference + * + * Sets the value of 'tree' by setting it to the given Vector. + * No type checking is performed. + * + * @param treeVector the Vector to copy. + */ + public void setTreeAsReference(java.util.Vector treeVector) + { + _treeList = treeVector; + } //-- void setTreeAsReference(java.util.Vector) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Alignment + */ + public static org.vamsas.client.objects.Alignment unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Alignment) Unmarshaller.unmarshal(org.vamsas.client.objects.Alignment.class, reader); + } //-- org.vamsas.client.objects.Alignment 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/client/objects/AlignmentAnnotations.java b/src/org/vamsas/client/objects/AlignmentAnnotations.java new file mode 100644 index 0000000..dda3f7b --- /dev/null +++ b/src/org/vamsas/client/objects/AlignmentAnnotations.java @@ -0,0 +1,506 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AlignmentAnnotations. + * + * @version $Revision$ $Date$ + */ +public class AlignmentAnnotations extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _graph + */ + private boolean _graph; + + /** + * keeps track of state for field: _graph + */ + private boolean _has_graph; + + /** + * Field _annotationElementList + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label + */ + private java.lang.String _label; + + /** + * Field _description + */ + private java.lang.String _description; + + /** + * Field _provenance + */ + private org.vamsas.client.objects.Provenance _provenance; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlignmentAnnotations() + { + super(); + _annotationElementList = new Vector(); + } //-- org.vamsas.client.objects.AlignmentAnnotations() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAnnotationElement + * + * + * + * @param vAnnotationElement + */ + public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + _annotationElementList.addElement(vAnnotationElement); + } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement) + + /** + * Method addAnnotationElement + * + * + * + * @param index + * @param vAnnotationElement + */ + public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + _annotationElementList.insertElementAt(vAnnotationElement, index); + } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) + + /** + * Method deleteGraph + * + */ + public void deleteGraph() + { + this._has_graph= false; + } //-- void deleteGraph() + + /** + * Method enumerateAnnotationElement + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAnnotationElement() + { + return _annotationElementList.elements(); + } //-- java.util.Enumeration enumerateAnnotationElement() + + /** + * 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 AlignmentAnnotations) { + + AlignmentAnnotations temp = (AlignmentAnnotations)obj; + if (this._graph != temp._graph) + return false; + if (this._has_graph != temp._has_graph) + return false; + if (this._annotationElementList != null) { + if (temp._annotationElementList == null) return false; + else if (!(this._annotationElementList.equals(temp._annotationElementList))) + return false; + } + else if (temp._annotationElementList != null) + return false; + if (this._label != null) { + if (temp._label == null) return false; + else if (!(this._label.equals(temp._label))) + return false; + } + else if (temp._label != null) + return false; + if (this._description != null) { + if (temp._description == null) return false; + else if (!(this._description.equals(temp._description))) + return false; + } + else if (temp._description != 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) + + /** + * Method getAnnotationElement + * + * + * + * @param index + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationElementList.size())) { + throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + } + + return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); + } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int) + + /** + * Method getAnnotationElement + * + * + * + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() + { + int size = _annotationElementList.size(); + org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() + + /** + * Method getAnnotationElementAsReference + * + * Returns a reference to 'annotationElement'. No type checking + * is performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getAnnotationElementAsReference() + { + return _annotationElementList; + } //-- java.util.Vector getAnnotationElementAsReference() + + /** + * Method getAnnotationElementCount + * + * + * + * @return int + */ + public int getAnnotationElementCount() + { + return _annotationElementList.size(); + } //-- int getAnnotationElementCount() + + /** + * Returns the value of field 'description'. + * + * @return String + * @return the value of field 'description'. + */ + public java.lang.String getDescription() + { + return this._description; + } //-- java.lang.String getDescription() + + /** + * Returns the value of field 'graph'. + * + * @return boolean + * @return the value of field 'graph'. + */ + public boolean getGraph() + { + return this._graph; + } //-- boolean getGraph() + + /** + * Returns the value of field 'label'. + * + * @return String + * @return the value of field 'label'. + */ + public java.lang.String getLabel() + { + return this._label; + } //-- java.lang.String getLabel() + + /** + * Returns the value of field 'provenance'. + * + * @return Provenance + * @return the value of field 'provenance'. + */ + public org.vamsas.client.objects.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.client.objects.Provenance getProvenance() + + /** + * Method hasGraph + * + * + * + * @return boolean + */ + public boolean hasGraph() + { + return this._has_graph; + } //-- boolean hasGraph() + + /** + * 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 removeAllAnnotationElement + * + */ + public void removeAllAnnotationElement() + { + _annotationElementList.removeAllElements(); + } //-- void removeAllAnnotationElement() + + /** + * Method removeAnnotationElement + * + * + * + * @param index + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index) + { + java.lang.Object obj = _annotationElementList.elementAt(index); + _annotationElementList.removeElementAt(index); + return (org.vamsas.client.objects.AnnotationElement) obj; + } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int) + + /** + * Method setAnnotationElement + * + * + * + * @param index + * @param vAnnotationElement + */ + public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationElementList.size())) { + throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + } + _annotationElementList.setElementAt(vAnnotationElement, index); + } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) + + /** + * Method setAnnotationElement + * + * + * + * @param annotationElementArray + */ + public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray) + { + //-- copy array + _annotationElementList.removeAllElements(); + for (int i = 0; i < annotationElementArray.length; i++) { + _annotationElementList.addElement(annotationElementArray[i]); + } + } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement) + + /** + * Method setAnnotationElement + * + * Sets the value of 'annotationElement' by copying the given + * Vector. + * + * @param annotationElementVector the Vector to copy. + */ + public void setAnnotationElement(java.util.Vector annotationElementVector) + { + //-- copy vector + _annotationElementList.removeAllElements(); + for (int i = 0; i < annotationElementVector.size(); i++) { + _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i)); + } + } //-- void setAnnotationElement(java.util.Vector) + + /** + * Method setAnnotationElementAsReference + * + * Sets the value of 'annotationElement' by setting it to the + * given Vector. No type checking is performed. + * + * @param annotationElementVector the Vector to copy. + */ + public void setAnnotationElementAsReference(java.util.Vector annotationElementVector) + { + _annotationElementList = annotationElementVector; + } //-- void setAnnotationElementAsReference(java.util.Vector) + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription(java.lang.String description) + { + this._description = description; + } //-- void setDescription(java.lang.String) + + /** + * Sets the value of field 'graph'. + * + * @param graph the value of field 'graph'. + */ + public void setGraph(boolean graph) + { + this._graph = graph; + this._has_graph = true; + } //-- void setGraph(boolean) + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel(java.lang.String label) + { + this._label = label; + } //-- void setLabel(java.lang.String) + + /** + * Sets the value of field 'provenance'. + * + * @param provenance the value of field 'provenance'. + */ + public void setProvenance(org.vamsas.client.objects.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.client.objects.Provenance) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return AlignmentAnnotations + */ + public static org.vamsas.client.objects.AlignmentAnnotations unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentAnnotations.class, reader); + } //-- org.vamsas.client.objects.AlignmentAnnotations 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/client/objects/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java new file mode 100644 index 0000000..9f10c38 --- /dev/null +++ b/src/org/vamsas/client/objects/AlignmentAnnotationsDescriptor.java @@ -0,0 +1,368 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AlignmentAnnotationsDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlignmentAnnotationsDescriptor 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 AlignmentAnnotationsDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "AlignmentAnnotations"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _graph + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + if(!target.hasGraph()) + return null; + return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + // ignore null values for non optional primitives + if (value == null) return; + + target.setGraph( ((java.lang.Boolean)value).booleanValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graph + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + BooleanValidator typeValidator = new BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _annotationElementList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + return target.getAnnotationElement(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.AnnotationElement(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationElementList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _label + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + return target.getLabel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + target.setLabel( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _label + 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); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + target.setDescription( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + 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.client.objects.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 + { + AlignmentAnnotations target = (AlignmentAnnotations) object; + return target.getProvenance(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentAnnotations target = (AlignmentAnnotations) object; + target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.AlignmentAnnotationsDescriptor() + + + //-----------/ + //- 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.client.objects.AlignmentAnnotations.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/client/objects/AlignmentDescriptor.java b/src/org/vamsas/client/objects/AlignmentDescriptor.java new file mode 100644 index 0000000..30326b7 --- /dev/null +++ b/src/org/vamsas/client/objects/AlignmentDescriptor.java @@ -0,0 +1,315 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AlignmentDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlignmentDescriptor 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 AlignmentDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "Alignment"; + + //-- 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 + + //-- _alignmentAnnotations + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentAnnotations.class, "_alignmentAnnotations", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alignment target = (Alignment) object; + return target.getAlignmentAnnotations(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alignment target = (Alignment) object; + target.setAlignmentAnnotations( (org.vamsas.client.objects.AlignmentAnnotations) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.AlignmentAnnotations(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _alignmentAnnotations + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alignment target = (Alignment) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alignment target = (Alignment) object; + target.addTree( (org.vamsas.client.objects.Tree) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Tree(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _alignmentSequenceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alignment target = (Alignment) object; + return target.getAlignmentSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alignment target = (Alignment) object; + target.addAlignmentSequence( (org.vamsas.client.objects.AlignmentSequence) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.AlignmentSequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alignmentSequenceList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(2); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _provenance + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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 + { + Alignment target = (Alignment) object; + return target.getProvenance(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alignment target = (Alignment) object; + target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.AlignmentDescriptor() + + + //-----------/ + //- 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.client.objects.Alignment.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/client/objects/AlignmentSequence.java b/src/org/vamsas/client/objects/AlignmentSequence.java new file mode 100644 index 0000000..30c7406 --- /dev/null +++ b/src/org/vamsas/client/objects/AlignmentSequence.java @@ -0,0 +1,179 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AlignmentSequence. + * + * @version $Revision$ $Date$ + */ +public class AlignmentSequence extends org.vamsas.client.objects.SequenceType +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id + */ + private java.lang.Object _id; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlignmentSequence() + { + super(); + } //-- org.vamsas.client.objects.AlignmentSequence() + + + //-----------/ + //- 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 AlignmentSequence) { + + AlignmentSequence temp = (AlignmentSequence)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; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'id'. + * + * @return Object + * @return the value of field 'id'. + */ + public java.lang.Object getId() + { + return this._id; + } //-- java.lang.Object getId() + + /** + * 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) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.Object id) + { + this._id = id; + } //-- void setId(java.lang.Object) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return SequenceType + */ + public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentSequence.class, reader); + } //-- org.vamsas.client.objects.SequenceType 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/client/objects/AlignmentSequenceDescriptor.java b/src/org/vamsas/client/objects/AlignmentSequenceDescriptor.java new file mode 100644 index 0000000..181ddf9 --- /dev/null +++ b/src/org/vamsas/client/objects/AlignmentSequenceDescriptor.java @@ -0,0 +1,210 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AlignmentSequenceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AlignmentSequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor { + + + //--------------------------/ + //- 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 AlignmentSequenceDescriptor() + { + super(); + setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor()); + nsURI = "http://www.vamsas.org"; + xmlName = "alignmentSequence"; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.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); + 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(); + } + 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); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.Object(); + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } //-- org.vamsas.client.objects.AlignmentSequenceDescriptor() + + + //-----------/ + //- 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.client.objects.AlignmentSequence.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/client/objects/AnnotationElement.java b/src/org/vamsas/client/objects/AnnotationElement.java new file mode 100644 index 0000000..90a994d --- /dev/null +++ b/src/org/vamsas/client/objects/AnnotationElement.java @@ -0,0 +1,360 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AnnotationElement. + * + * @version $Revision$ $Date$ + */ +public class AnnotationElement extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _position + */ + private int _position; + + /** + * keeps track of state for field: _position + */ + private boolean _has_position; + + /** + * Field _displayCharacter + */ + private java.lang.String _displayCharacter; + + /** + * Field _description + */ + private java.lang.String _description; + + /** + * Field _secondaryStructure + */ + private java.lang.String _secondaryStructure; + + /** + * Field _value + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElement() + { + super(); + } //-- org.vamsas.client.objects.AnnotationElement() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method deletePosition + * + */ + public void deletePosition() + { + this._has_position= false; + } //-- void deletePosition() + + /** + * Method deleteValue + * + */ + public void deleteValue() + { + this._has_value= false; + } //-- void deleteValue() + + /** + * 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 AnnotationElement) { + + AnnotationElement temp = (AnnotationElement)obj; + if (this._position != temp._position) + return false; + if (this._has_position != temp._has_position) + return false; + if (this._displayCharacter != null) { + if (temp._displayCharacter == null) return false; + else if (!(this._displayCharacter.equals(temp._displayCharacter))) + return false; + } + else if (temp._displayCharacter != null) + return false; + if (this._description != null) { + if (temp._description == null) return false; + else if (!(this._description.equals(temp._description))) + return false; + } + else if (temp._description != null) + return false; + if (this._secondaryStructure != null) { + if (temp._secondaryStructure == null) return false; + else if (!(this._secondaryStructure.equals(temp._secondaryStructure))) + return false; + } + else if (temp._secondaryStructure != null) + return false; + if (this._value != temp._value) + return false; + if (this._has_value != temp._has_value) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'description'. + * + * @return String + * @return the value of field 'description'. + */ + public java.lang.String getDescription() + { + return this._description; + } //-- java.lang.String getDescription() + + /** + * Returns the value of field 'displayCharacter'. + * + * @return String + * @return the value of field 'displayCharacter'. + */ + public java.lang.String getDisplayCharacter() + { + return this._displayCharacter; + } //-- java.lang.String getDisplayCharacter() + + /** + * Returns the value of field 'position'. + * + * @return int + * @return the value of field 'position'. + */ + public int getPosition() + { + return this._position; + } //-- int getPosition() + + /** + * Returns the value of field 'secondaryStructure'. + * + * @return String + * @return the value of field 'secondaryStructure'. + */ + public java.lang.String getSecondaryStructure() + { + return this._secondaryStructure; + } //-- java.lang.String getSecondaryStructure() + + /** + * Returns the value of field 'value'. + * + * @return float + * @return the value of field 'value'. + */ + public float getValue() + { + return this._value; + } //-- float getValue() + + /** + * Method hasPosition + * + * + * + * @return boolean + */ + public boolean hasPosition() + { + return this._has_position; + } //-- boolean hasPosition() + + /** + * Method hasValue + * + * + * + * @return boolean + */ + public boolean hasValue() + { + return this._has_value; + } //-- boolean hasValue() + + /** + * 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) + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription(java.lang.String description) + { + this._description = description; + } //-- void setDescription(java.lang.String) + + /** + * Sets the value of field 'displayCharacter'. + * + * @param displayCharacter the value of field 'displayCharacter' + */ + public void setDisplayCharacter(java.lang.String displayCharacter) + { + this._displayCharacter = displayCharacter; + } //-- void setDisplayCharacter(java.lang.String) + + /** + * Sets the value of field 'position'. + * + * @param position the value of field 'position'. + */ + public void setPosition(int position) + { + this._position = position; + this._has_position = true; + } //-- void setPosition(int) + + /** + * Sets the value of field 'secondaryStructure'. + * + * @param secondaryStructure the value of field + * 'secondaryStructure'. + */ + public void setSecondaryStructure(java.lang.String secondaryStructure) + { + this._secondaryStructure = secondaryStructure; + } //-- void setSecondaryStructure(java.lang.String) + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue(float value) + { + this._value = value; + this._has_value = true; + } //-- void setValue(float) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return AnnotationElement + */ + public static org.vamsas.client.objects.AnnotationElement unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.client.objects.AnnotationElement.class, reader); + } //-- org.vamsas.client.objects.AnnotationElement 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/client/objects/AnnotationElementDescriptor.java b/src/org/vamsas/client/objects/AnnotationElementDescriptor.java new file mode 100644 index 0000000..b07683a --- /dev/null +++ b/src/org/vamsas/client/objects/AnnotationElementDescriptor.java @@ -0,0 +1,380 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 AnnotationElementDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AnnotationElementDescriptor 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 AnnotationElementDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "annotationElement"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _position + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if(!target.hasPosition()) + return null; + return new java.lang.Integer(target.getPosition()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // ignore null values for non optional primitives + if (value == null) return; + + target.setPosition( ((java.lang.Integer)value).intValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _position + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + IntegerValidator typeValidator= new IntegerValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _displayCharacter + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDisplayCharacter(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDisplayCharacter( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayCharacter + 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); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDescription( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + 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); + //-- _secondaryStructure + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getSecondaryStructure(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setSecondaryStructure( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _secondaryStructure + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setLength(1); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if(!target.hasValue()) + return null; + return new java.lang.Float(target.getValue()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // ignore null values for non optional primitives + if (value == null) return; + + target.setValue( ((java.lang.Float)value).floatValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + FloatValidator typeValidator = new FloatValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.AnnotationElementDescriptor() + + + //-----------/ + //- 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.client.objects.AnnotationElement.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/client/objects/Application.java b/src/org/vamsas/client/objects/Application.java new file mode 100644 index 0000000..1906c33 --- /dev/null +++ b/src/org/vamsas/client/objects/Application.java @@ -0,0 +1,212 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Application. + * + * @version $Revision$ $Date$ + */ +public class Application extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _version + */ + private java.lang.Object _version; + + /** + * Field _name + */ + private java.lang.Object _name; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Application() + { + super(); + } //-- org.vamsas.client.objects.Application() + + + //-----------/ + //- 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 Application) { + + Application temp = (Application)obj; + if (this._version != null) { + if (temp._version == null) return false; + else if (!(this._version.equals(temp._version))) + return false; + } + else if (temp._version != null) + return false; + if (this._name != null) { + if (temp._name == null) return false; + else if (!(this._name.equals(temp._name))) + return false; + } + else if (temp._name != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'name'. + * + * @return Object + * @return the value of field 'name'. + */ + public java.lang.Object getName() + { + return this._name; + } //-- java.lang.Object getName() + + /** + * Returns the value of field 'version'. + * + * @return Object + * @return the value of field 'version'. + */ + public java.lang.Object getVersion() + { + return this._version; + } //-- java.lang.Object getVersion() + + /** + * 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) + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName(java.lang.Object name) + { + this._name = name; + } //-- void setName(java.lang.Object) + + /** + * Sets the value of field 'version'. + * + * @param version the value of field 'version'. + */ + public void setVersion(java.lang.Object version) + { + this._version = version; + } //-- void setVersion(java.lang.Object) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Application + */ + public static org.vamsas.client.objects.Application unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Application) Unmarshaller.unmarshal(org.vamsas.client.objects.Application.class, reader); + } //-- org.vamsas.client.objects.Application 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/client/objects/ApplicationData.java b/src/org/vamsas/client/objects/ApplicationData.java new file mode 100644 index 0000000..ba3a87f --- /dev/null +++ b/src/org/vamsas/client/objects/ApplicationData.java @@ -0,0 +1,179 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 ApplicationData. + * + * @version $Revision$ $Date$ + */ +public class ApplicationData extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _application + */ + private org.vamsas.client.objects.Application _application; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ApplicationData() + { + super(); + } //-- org.vamsas.client.objects.ApplicationData() + + + //-----------/ + //- 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 ApplicationData) { + + ApplicationData temp = (ApplicationData)obj; + if (this._application != null) { + if (temp._application == null) return false; + else if (!(this._application.equals(temp._application))) + return false; + } + else if (temp._application != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'application'. + * + * @return Application + * @return the value of field 'application'. + */ + public org.vamsas.client.objects.Application getApplication() + { + return this._application; + } //-- org.vamsas.client.objects.Application getApplication() + + /** + * 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) + + /** + * Sets the value of field 'application'. + * + * @param application the value of field 'application'. + */ + public void setApplication(org.vamsas.client.objects.Application application) + { + this._application = application; + } //-- void setApplication(org.vamsas.client.objects.Application) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return ApplicationData + */ + public static org.vamsas.client.objects.ApplicationData unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.ApplicationData) Unmarshaller.unmarshal(org.vamsas.client.objects.ApplicationData.class, reader); + } //-- org.vamsas.client.objects.ApplicationData 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/client/objects/ApplicationDataDescriptor.java b/src/org/vamsas/client/objects/ApplicationDataDescriptor.java new file mode 100644 index 0000000..1854106 --- /dev/null +++ b/src/org/vamsas/client/objects/ApplicationDataDescriptor.java @@ -0,0 +1,210 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 ApplicationDataDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ApplicationDataDescriptor 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 ApplicationDataDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "ApplicationData"; + + //-- 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 + + //-- _application + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Application.class, "_application", "Application", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ApplicationData target = (ApplicationData) object; + return target.getApplication(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ApplicationData target = (ApplicationData) object; + target.setApplication( (org.vamsas.client.objects.Application) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Application(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _application + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.ApplicationDataDescriptor() + + + //-----------/ + //- 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.client.objects.ApplicationData.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/client/objects/ApplicationDescriptor.java b/src/org/vamsas/client/objects/ApplicationDescriptor.java new file mode 100644 index 0000000..916d9e1 --- /dev/null +++ b/src/org/vamsas/client/objects/ApplicationDescriptor.java @@ -0,0 +1,237 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 ApplicationDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ApplicationDescriptor 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 ApplicationDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "Application"; + 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 + + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Application target = (Application) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Application target = (Application) object; + target.setVersion( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Application target = (Application) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Application target = (Application) object; + target.setName( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } //-- org.vamsas.client.objects.ApplicationDescriptor() + + + //-----------/ + //- 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.client.objects.Application.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/client/objects/DbRef.java b/src/org/vamsas/client/objects/DbRef.java new file mode 100644 index 0000000..4611077 --- /dev/null +++ b/src/org/vamsas/client/objects/DbRef.java @@ -0,0 +1,245 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 DbRef. + * + * @version $Revision$ $Date$ + */ +public class DbRef extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _source + */ + private java.lang.Object _source; + + /** + * Field _version + */ + private java.lang.Object _version; + + /** + * Field _accessionId + */ + private java.lang.Object _accessionId; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DbRef() + { + super(); + } //-- org.vamsas.client.objects.DbRef() + + + //-----------/ + //- 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 DbRef) { + + DbRef temp = (DbRef)obj; + if (this._source != null) { + if (temp._source == null) return false; + else if (!(this._source.equals(temp._source))) + return false; + } + else if (temp._source != null) + return false; + if (this._version != null) { + if (temp._version == null) return false; + else if (!(this._version.equals(temp._version))) + return false; + } + else if (temp._version != null) + return false; + if (this._accessionId != null) { + if (temp._accessionId == null) return false; + else if (!(this._accessionId.equals(temp._accessionId))) + return false; + } + else if (temp._accessionId != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'accessionId'. + * + * @return Object + * @return the value of field 'accessionId'. + */ + public java.lang.Object getAccessionId() + { + return this._accessionId; + } //-- java.lang.Object getAccessionId() + + /** + * Returns the value of field 'source'. + * + * @return Object + * @return the value of field 'source'. + */ + public java.lang.Object getSource() + { + return this._source; + } //-- java.lang.Object getSource() + + /** + * Returns the value of field 'version'. + * + * @return Object + * @return the value of field 'version'. + */ + public java.lang.Object getVersion() + { + return this._version; + } //-- java.lang.Object getVersion() + + /** + * 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) + + /** + * Sets the value of field 'accessionId'. + * + * @param accessionId the value of field 'accessionId'. + */ + public void setAccessionId(java.lang.Object accessionId) + { + this._accessionId = accessionId; + } //-- void setAccessionId(java.lang.Object) + + /** + * Sets the value of field 'source'. + * + * @param source the value of field 'source'. + */ + public void setSource(java.lang.Object source) + { + this._source = source; + } //-- void setSource(java.lang.Object) + + /** + * Sets the value of field 'version'. + * + * @param version the value of field 'version'. + */ + public void setVersion(java.lang.Object version) + { + this._version = version; + } //-- void setVersion(java.lang.Object) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return DbRef + */ + public static org.vamsas.client.objects.DbRef unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.DbRef) Unmarshaller.unmarshal(org.vamsas.client.objects.DbRef.class, reader); + } //-- org.vamsas.client.objects.DbRef 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/client/objects/DbRefDescriptor.java b/src/org/vamsas/client/objects/DbRefDescriptor.java new file mode 100644 index 0000000..fc646c4 --- /dev/null +++ b/src/org/vamsas/client/objects/DbRefDescriptor.java @@ -0,0 +1,270 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 DbRefDescriptor. + * + * @version $Revision$ $Date$ + */ +public class DbRefDescriptor 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 DbRefDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "dbRef"; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _source + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DbRef target = (DbRef) object; + return target.getSource(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DbRef target = (DbRef) object; + target.setSource( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _source + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DbRef target = (DbRef) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DbRef target = (DbRef) object; + target.setVersion( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _accessionId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DbRef target = (DbRef) object; + return target.getAccessionId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DbRef target = (DbRef) object; + target.setAccessionId( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _accessionId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } //-- org.vamsas.client.objects.DbRefDescriptor() + + + //-----------/ + //- 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.client.objects.DbRef.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/client/objects/Entry.java b/src/org/vamsas/client/objects/Entry.java new file mode 100644 index 0000000..9bf7b67 --- /dev/null +++ b/src/org/vamsas/client/objects/Entry.java @@ -0,0 +1,245 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Entry. + * + * @version $Revision$ $Date$ + */ +public class Entry extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _user + */ + private java.lang.String _user; + + /** + * Field _action + */ + private java.lang.String _action; + + /** + * Field _date + */ + private org.exolab.castor.types.Date _date; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Entry() + { + super(); + } //-- org.vamsas.client.objects.Entry() + + + //-----------/ + //- 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 Entry) { + + Entry temp = (Entry)obj; + if (this._user != null) { + if (temp._user == null) return false; + else if (!(this._user.equals(temp._user))) + return false; + } + else if (temp._user != null) + return false; + if (this._action != null) { + if (temp._action == null) return false; + else if (!(this._action.equals(temp._action))) + return false; + } + else if (temp._action != null) + return false; + if (this._date != null) { + if (temp._date == null) return false; + else if (!(this._date.equals(temp._date))) + return false; + } + else if (temp._date != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'action'. + * + * @return String + * @return the value of field 'action'. + */ + public java.lang.String getAction() + { + return this._action; + } //-- java.lang.String getAction() + + /** + * Returns the value of field 'date'. + * + * @return Date + * @return the value of field 'date'. + */ + public org.exolab.castor.types.Date getDate() + { + return this._date; + } //-- org.exolab.castor.types.Date getDate() + + /** + * Returns the value of field 'user'. + * + * @return String + * @return the value of field 'user'. + */ + public java.lang.String getUser() + { + return this._user; + } //-- java.lang.String getUser() + + /** + * 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) + + /** + * Sets the value of field 'action'. + * + * @param action the value of field 'action'. + */ + public void setAction(java.lang.String action) + { + this._action = action; + } //-- void setAction(java.lang.String) + + /** + * Sets the value of field 'date'. + * + * @param date the value of field 'date'. + */ + public void setDate(org.exolab.castor.types.Date date) + { + this._date = date; + } //-- void setDate(org.exolab.castor.types.Date) + + /** + * Sets the value of field 'user'. + * + * @param user the value of field 'user'. + */ + public void setUser(java.lang.String user) + { + this._user = user; + } //-- void setUser(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Entry + */ + public static org.vamsas.client.objects.Entry unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Entry) Unmarshaller.unmarshal(org.vamsas.client.objects.Entry.class, reader); + } //-- org.vamsas.client.objects.Entry 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/client/objects/EntryDescriptor.java b/src/org/vamsas/client/objects/EntryDescriptor.java new file mode 100644 index 0000000..5a4f726 --- /dev/null +++ b/src/org/vamsas/client/objects/EntryDescriptor.java @@ -0,0 +1,292 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 EntryDescriptor. + * + * @version $Revision$ $Date$ + */ +public class EntryDescriptor 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 EntryDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "entry"; + + //-- 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 + + //-- _user + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Entry target = (Entry) object; + return target.getUser(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Entry target = (Entry) object; + target.setUser( (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: _user + 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); + //-- _action + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Entry target = (Entry) object; + return target.getAction(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Entry target = (Entry) object; + target.setAction( (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: _action + 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); + //-- _date + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Entry target = (Entry) object; + return target.getDate(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Entry target = (Entry) object; + target.setDate( (org.exolab.castor.types.Date) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.exolab.castor.types.Date(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _date + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + DateTimeValidator typeValidator = new DateTimeValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.EntryDescriptor() + + + //-----------/ + //- 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.client.objects.Entry.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/client/objects/LockFile.java b/src/org/vamsas/client/objects/LockFile.java new file mode 100644 index 0000000..257710d --- /dev/null +++ b/src/org/vamsas/client/objects/LockFile.java @@ -0,0 +1,182 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 LockFile. + * + * @version $Revision$ $Date$ + */ +public class LockFile extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * internal content storage + */ + private java.lang.String _content = ""; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public LockFile() + { + super(); + setContent(""); + } //-- org.vamsas.client.objects.LockFile() + + + //-----------/ + //- 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 LockFile) { + + LockFile temp = (LockFile)obj; + if (this._content != null) { + if (temp._content == null) return false; + else if (!(this._content.equals(temp._content))) + return false; + } + else if (temp._content != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'content'. The field 'content' + * has the following description: internal content storage + * + * @return String + * @return the value of field 'content'. + */ + public java.lang.String getContent() + { + return this._content; + } //-- java.lang.String getContent() + + /** + * 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) + + /** + * Sets the value of field 'content'. The field 'content' has + * the following description: internal content storage + * + * @param content the value of field 'content'. + */ + public void setContent(java.lang.String content) + { + this._content = content; + } //-- void setContent(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return LockFile + */ + public static org.vamsas.client.objects.LockFile unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.LockFile) Unmarshaller.unmarshal(org.vamsas.client.objects.LockFile.class, reader); + } //-- org.vamsas.client.objects.LockFile 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/client/objects/LockFileDescriptor.java b/src/org/vamsas/client/objects/LockFileDescriptor.java new file mode 100644 index 0000000..8a5f5d9 --- /dev/null +++ b/src/org/vamsas/client/objects/LockFileDescriptor.java @@ -0,0 +1,207 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 LockFileDescriptor. + * + * @version $Revision$ $Date$ + */ +public class LockFileDescriptor 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 LockFileDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "LockFile"; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- _content + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + LockFile target = (LockFile) object; + return target.getContent(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + LockFile target = (LockFile) object; + target.setContent( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _content + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize attribute descriptors + + //-- initialize element descriptors + + } //-- org.vamsas.client.objects.LockFileDescriptor() + + + //-----------/ + //- 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.client.objects.LockFile.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/client/objects/Provenance.java b/src/org/vamsas/client/objects/Provenance.java new file mode 100644 index 0000000..62da458 --- /dev/null +++ b/src/org/vamsas/client/objects/Provenance.java @@ -0,0 +1,350 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Provenance. + * + * @version $Revision$ $Date$ + */ +public class Provenance extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _items + */ + private java.util.Vector _items; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Provenance() + { + super(); + _items = new Vector(); + } //-- org.vamsas.client.objects.Provenance() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addProvenanceItem + * + * + * + * @param vProvenanceItem + */ + public void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem vProvenanceItem) + throws java.lang.IndexOutOfBoundsException + { + _items.addElement(vProvenanceItem); + } //-- void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem) + + /** + * Method addProvenanceItem + * + * + * + * @param index + * @param vProvenanceItem + */ + public void addProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem) + throws java.lang.IndexOutOfBoundsException + { + _items.insertElementAt(vProvenanceItem, index); + } //-- void addProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem) + + /** + * Method enumerateProvenanceItem + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateProvenanceItem() + { + return _items.elements(); + } //-- java.util.Enumeration enumerateProvenanceItem() + + /** + * 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 Provenance) { + + Provenance temp = (Provenance)obj; + if (this._items != null) { + if (temp._items == null) return false; + else if (!(this._items.equals(temp._items))) + return false; + } + else if (temp._items != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Method getProvenanceItem + * + * + * + * @param index + * @return ProvenanceItem + */ + public org.vamsas.client.objects.ProvenanceItem getProvenanceItem(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _items.size())) { + throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); + } + + return (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index); + } //-- org.vamsas.client.objects.ProvenanceItem getProvenanceItem(int) + + /** + * Method getProvenanceItem + * + * + * + * @return ProvenanceItem + */ + public org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem() + { + int size = _items.size(); + org.vamsas.client.objects.ProvenanceItem[] mArray = new org.vamsas.client.objects.ProvenanceItem[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem() + + /** + * Method getProvenanceItemAsReference + * + * Returns a reference to 'provenanceItem'. No type checking is + * performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getProvenanceItemAsReference() + { + return _items; + } //-- java.util.Vector getProvenanceItemAsReference() + + /** + * Method getProvenanceItemCount + * + * + * + * @return int + */ + public int getProvenanceItemCount() + { + return _items.size(); + } //-- int getProvenanceItemCount() + + /** + * 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 removeAllProvenanceItem + * + */ + public void removeAllProvenanceItem() + { + _items.removeAllElements(); + } //-- void removeAllProvenanceItem() + + /** + * Method removeProvenanceItem + * + * + * + * @param index + * @return ProvenanceItem + */ + public org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int index) + { + java.lang.Object obj = _items.elementAt(index); + _items.removeElementAt(index); + return (org.vamsas.client.objects.ProvenanceItem) obj; + } //-- org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int) + + /** + * Method setProvenanceItem + * + * + * + * @param index + * @param vProvenanceItem + */ + public void setProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _items.size())) { + throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); + } + _items.setElementAt(vProvenanceItem, index); + } //-- void setProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem) + + /** + * Method setProvenanceItem + * + * + * + * @param provenanceItemArray + */ + public void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem[] provenanceItemArray) + { + //-- copy array + _items.removeAllElements(); + for (int i = 0; i < provenanceItemArray.length; i++) { + _items.addElement(provenanceItemArray[i]); + } + } //-- void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem) + + /** + * Method setProvenanceItem + * + * Sets the value of 'provenanceItem' by copying the given + * Vector. + * + * @param provenanceItemVector the Vector to copy. + */ + public void setProvenanceItem(java.util.Vector provenanceItemVector) + { + //-- copy vector + _items.removeAllElements(); + for (int i = 0; i < provenanceItemVector.size(); i++) { + _items.addElement((org.vamsas.client.objects.ProvenanceItem)provenanceItemVector.elementAt(i)); + } + } //-- void setProvenanceItem(java.util.Vector) + + /** + * Method setProvenanceItemAsReference + * + * Sets the value of 'provenanceItem' by setting it to the + * given Vector. No type checking is performed. + * + * @param provenanceItemVector the Vector to copy. + */ + public void setProvenanceItemAsReference(java.util.Vector provenanceItemVector) + { + _items = provenanceItemVector; + } //-- void setProvenanceItemAsReference(java.util.Vector) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Provenance + */ + public static org.vamsas.client.objects.Provenance unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Provenance) Unmarshaller.unmarshal(org.vamsas.client.objects.Provenance.class, reader); + } //-- org.vamsas.client.objects.Provenance 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/client/objects/ProvenanceDescriptor.java b/src/org/vamsas/client/objects/ProvenanceDescriptor.java new file mode 100644 index 0000000..d9bfe17 --- /dev/null +++ b/src/org/vamsas/client/objects/ProvenanceDescriptor.java @@ -0,0 +1,206 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 ProvenanceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ProvenanceDescriptor 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 ProvenanceDescriptor() + { + super(); + xmlName = "Provenance"; + 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 + + //-- _items + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.ProvenanceItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Provenance target = (Provenance) object; + return target.getProvenanceItem(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Provenance target = (Provenance) object; + target.addProvenanceItem( (org.vamsas.client.objects.ProvenanceItem) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.ProvenanceItem(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new org.vamsas.client.objects.ProvenanceItemDescriptor()); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _items + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.ProvenanceDescriptor() + + + //-----------/ + //- 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.client.objects.Provenance.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/client/objects/ProvenanceItem.java b/src/org/vamsas/client/objects/ProvenanceItem.java new file mode 100644 index 0000000..963afe6 --- /dev/null +++ b/src/org/vamsas/client/objects/ProvenanceItem.java @@ -0,0 +1,71 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.Serializable; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class ProvenanceItem. + * + * @version $Revision$ $Date$ + */ +public class ProvenanceItem implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _entry + */ + private org.vamsas.client.objects.Entry _entry; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ProvenanceItem() + { + super(); + } //-- org.vamsas.client.objects.ProvenanceItem() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'entry'. + * + * @return Entry + * @return the value of field 'entry'. + */ + public org.vamsas.client.objects.Entry getEntry() + { + return this._entry; + } //-- org.vamsas.client.objects.Entry getEntry() + + /** + * Sets the value of field 'entry'. + * + * @param entry the value of field 'entry'. + */ + public void setEntry(org.vamsas.client.objects.Entry entry) + { + this._entry = entry; + } //-- void setEntry(org.vamsas.client.objects.Entry) + +} diff --git a/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java b/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java new file mode 100644 index 0000000..b7ffd98 --- /dev/null +++ b/src/org/vamsas/client/objects/ProvenanceItemDescriptor.java @@ -0,0 +1,210 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 ProvenanceItemDescriptor. + * + * @version $Revision$ $Date$ + */ +public class ProvenanceItemDescriptor 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 ProvenanceItemDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "Provenance"; + + //-- 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 + + //-- _entry + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Entry.class, "_entry", "entry", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ProvenanceItem target = (ProvenanceItem) object; + return target.getEntry(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ProvenanceItem target = (ProvenanceItem) object; + target.setEntry( (org.vamsas.client.objects.Entry) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Entry(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _entry + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.ProvenanceItemDescriptor() + + + //-----------/ + //- 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.client.objects.ProvenanceItem.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/client/objects/Sequence.java b/src/org/vamsas/client/objects/Sequence.java new file mode 100644 index 0000000..8466e69 --- /dev/null +++ b/src/org/vamsas/client/objects/Sequence.java @@ -0,0 +1,212 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Sequence. + * + * @version $Revision$ $Date$ + */ +public class Sequence extends org.vamsas.client.objects.SequenceType +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _dictionary + */ + private java.lang.String _dictionary; + + /** + * Field _id + */ + private java.lang.String _id; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() + { + super(); + } //-- org.vamsas.client.objects.Sequence() + + + //-----------/ + //- 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 Sequence) { + + Sequence temp = (Sequence)obj; + if (this._dictionary != null) { + if (temp._dictionary == null) return false; + else if (!(this._dictionary.equals(temp._dictionary))) + return false; + } + 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; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'dictionary'. + * + * @return String + * @return the value of field 'dictionary'. + */ + public java.lang.String getDictionary() + { + return this._dictionary; + } //-- 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 + * + * + * + * @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) + + /** + * Sets the value of field 'dictionary'. + * + * @param dictionary the value of field 'dictionary'. + */ + public void setDictionary(java.lang.String dictionary) + { + this._dictionary = dictionary; + } //-- 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 + * + * + * + * @param reader + * @return SequenceType + */ + public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Sequence) Unmarshaller.unmarshal(org.vamsas.client.objects.Sequence.class, reader); + } //-- org.vamsas.client.objects.SequenceType 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/client/objects/SequenceDescriptor.java b/src/org/vamsas/client/objects/SequenceDescriptor.java new file mode 100644 index 0000000..95df6e0 --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceDescriptor.java @@ -0,0 +1,247 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor { + + + //--------------------------/ + //- 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 SequenceDescriptor() + { + super(); + setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor()); + nsURI = "http://www.vamsas.org"; + xmlName = "Sequence"; + 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 + + //-- _dictionary + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDictionary(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.setDictionary( (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: _dictionary + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + 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.client.objects.SequenceDescriptor() + + + //-----------/ + //- 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.client.objects.Sequence.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/client/objects/SequenceSet.java b/src/org/vamsas/client/objects/SequenceSet.java new file mode 100644 index 0000000..d78ce6b --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceSet.java @@ -0,0 +1,908 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceSet. + * + * @version $Revision$ $Date$ + */ +public class SequenceSet extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _gapChar + */ + private java.lang.String _gapChar; + + /** + * Field _aligned + */ + private boolean _aligned; + + /** + * keeps track of state for field: _aligned + */ + private boolean _has_aligned; + + /** + * Field _sequenceList + */ + private java.util.Vector _sequenceList; + + /** + * Field _sequenceSetAnnotationsList + */ + private java.util.Vector _sequenceSetAnnotationsList; + + /** + * Field _alignmentList + */ + private java.util.Vector _alignmentList; + + /** + * Field _tree + */ + private org.vamsas.client.objects.Tree _tree; + + /** + * Field _provenance + */ + private org.vamsas.client.objects.Provenance _provenance; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSet() + { + super(); + _sequenceList = new Vector(); + _sequenceSetAnnotationsList = new Vector(); + _alignmentList = new Vector(); + } //-- org.vamsas.client.objects.SequenceSet() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAlignment + * + * + * + * @param vAlignment + */ + public void addAlignment(org.vamsas.client.objects.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + _alignmentList.addElement(vAlignment); + } //-- void addAlignment(org.vamsas.client.objects.Alignment) + + /** + * Method addAlignment + * + * + * + * @param index + * @param vAlignment + */ + public void addAlignment(int index, org.vamsas.client.objects.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + _alignmentList.insertElementAt(vAlignment, index); + } //-- void addAlignment(int, org.vamsas.client.objects.Alignment) + + /** + * Method addSequence + * + * + * + * @param vSequence + */ + public void addSequence(org.vamsas.client.objects.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + _sequenceList.addElement(vSequence); + } //-- void addSequence(org.vamsas.client.objects.Sequence) + + /** + * Method addSequence + * + * + * + * @param index + * @param vSequence + */ + public void addSequence(int index, org.vamsas.client.objects.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + _sequenceList.insertElementAt(vSequence, index); + } //-- void addSequence(int, org.vamsas.client.objects.Sequence) + + /** + * Method addSequenceSetAnnotations + * + * + * + * @param vSequenceSetAnnotations + */ + public void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations); + } //-- void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations) + + /** + * Method addSequenceSetAnnotations + * + * + * + * @param index + * @param vSequenceSetAnnotations + */ + public void addSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index); + } //-- void addSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations) + + /** + * Method deleteAligned + * + */ + public void deleteAligned() + { + this._has_aligned= false; + } //-- void deleteAligned() + + /** + * Method enumerateAlignment + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAlignment() + { + return _alignmentList.elements(); + } //-- java.util.Enumeration enumerateAlignment() + + /** + * Method enumerateSequence + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSequence() + { + return _sequenceList.elements(); + } //-- java.util.Enumeration enumerateSequence() + + /** + * Method enumerateSequenceSetAnnotations + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSequenceSetAnnotations() + { + return _sequenceSetAnnotationsList.elements(); + } //-- java.util.Enumeration enumerateSequenceSetAnnotations() + + /** + * 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 SequenceSet) { + + SequenceSet temp = (SequenceSet)obj; + if (this._gapChar != null) { + if (temp._gapChar == null) return false; + else if (!(this._gapChar.equals(temp._gapChar))) + return false; + } + else if (temp._gapChar != null) + return false; + if (this._aligned != temp._aligned) + return false; + if (this._has_aligned != temp._has_aligned) + return false; + if (this._sequenceList != null) { + if (temp._sequenceList == null) return false; + else if (!(this._sequenceList.equals(temp._sequenceList))) + return false; + } + else if (temp._sequenceList != null) + return false; + if (this._sequenceSetAnnotationsList != null) { + if (temp._sequenceSetAnnotationsList == null) return false; + else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList))) + return false; + } + else if (temp._sequenceSetAnnotationsList != null) + return false; + if (this._alignmentList != null) { + if (temp._alignmentList == null) return false; + else if (!(this._alignmentList.equals(temp._alignmentList))) + return false; + } + else if (temp._alignmentList != null) + return false; + if (this._tree != null) { + if (temp._tree == null) return false; + else if (!(this._tree.equals(temp._tree))) + return false; + } + else if (temp._tree != 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 'aligned'. + * + * @return boolean + * @return the value of field 'aligned'. + */ + public boolean getAligned() + { + return this._aligned; + } //-- boolean getAligned() + + /** + * Method getAlignment + * + * + * + * @param index + * @return Alignment + */ + public org.vamsas.client.objects.Alignment getAlignment(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentList.size())) { + throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); + } + + return (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index); + } //-- org.vamsas.client.objects.Alignment getAlignment(int) + + /** + * Method getAlignment + * + * + * + * @return Alignment + */ + public org.vamsas.client.objects.Alignment[] getAlignment() + { + int size = _alignmentList.size(); + org.vamsas.client.objects.Alignment[] mArray = new org.vamsas.client.objects.Alignment[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.Alignment[] getAlignment() + + /** + * Method getAlignmentAsReference + * + * Returns a reference to 'alignment'. No type checking is + * performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getAlignmentAsReference() + { + return _alignmentList; + } //-- java.util.Vector getAlignmentAsReference() + + /** + * Method getAlignmentCount + * + * + * + * @return int + */ + public int getAlignmentCount() + { + return _alignmentList.size(); + } //-- int getAlignmentCount() + + /** + * Returns the value of field 'gapChar'. + * + * @return String + * @return the value of field 'gapChar'. + */ + public java.lang.String getGapChar() + { + return this._gapChar; + } //-- java.lang.String getGapChar() + + /** + * Returns the value of field 'provenance'. + * + * @return Provenance + * @return the value of field 'provenance'. + */ + public org.vamsas.client.objects.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.client.objects.Provenance getProvenance() + + /** + * Method getSequence + * + * + * + * @param index + * @return Sequence + */ + public org.vamsas.client.objects.Sequence getSequence(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceList.size())) { + throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); + } + + return (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index); + } //-- org.vamsas.client.objects.Sequence getSequence(int) + + /** + * Method getSequence + * + * + * + * @return Sequence + */ + public org.vamsas.client.objects.Sequence[] getSequence() + { + int size = _sequenceList.size(); + org.vamsas.client.objects.Sequence[] mArray = new org.vamsas.client.objects.Sequence[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.Sequence[] getSequence() + + /** + * Method getSequenceAsReference + * + * Returns a reference to 'sequence'. No type checking is + * performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getSequenceAsReference() + { + return _sequenceList; + } //-- java.util.Vector getSequenceAsReference() + + /** + * Method getSequenceCount + * + * + * + * @return int + */ + public int getSequenceCount() + { + return _sequenceList.size(); + } //-- int getSequenceCount() + + /** + * Method getSequenceSetAnnotations + * + * + * + * @param index + * @return SequenceSetAnnotations + */ + public org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) { + throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]"); + } + + return (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index); + } //-- org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int) + + /** + * Method getSequenceSetAnnotations + * + * + * + * @return SequenceSetAnnotations + */ + public org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations() + { + int size = _sequenceSetAnnotationsList.size(); + org.vamsas.client.objects.SequenceSetAnnotations[] mArray = new org.vamsas.client.objects.SequenceSetAnnotations[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations() + + /** + * Method getSequenceSetAnnotationsAsReference + * + * Returns a reference to 'sequenceSetAnnotations'. No type + * checking is performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getSequenceSetAnnotationsAsReference() + { + return _sequenceSetAnnotationsList; + } //-- java.util.Vector getSequenceSetAnnotationsAsReference() + + /** + * Method getSequenceSetAnnotationsCount + * + * + * + * @return int + */ + public int getSequenceSetAnnotationsCount() + { + return _sequenceSetAnnotationsList.size(); + } //-- int getSequenceSetAnnotationsCount() + + /** + * Returns the value of field 'tree'. + * + * @return Tree + * @return the value of field 'tree'. + */ + public org.vamsas.client.objects.Tree getTree() + { + return this._tree; + } //-- org.vamsas.client.objects.Tree getTree() + + /** + * Method hasAligned + * + * + * + * @return boolean + */ + public boolean hasAligned() + { + return this._has_aligned; + } //-- boolean hasAligned() + + /** + * 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 removeAlignment + * + * + * + * @param index + * @return Alignment + */ + public org.vamsas.client.objects.Alignment removeAlignment(int index) + { + java.lang.Object obj = _alignmentList.elementAt(index); + _alignmentList.removeElementAt(index); + return (org.vamsas.client.objects.Alignment) obj; + } //-- org.vamsas.client.objects.Alignment removeAlignment(int) + + /** + * Method removeAllAlignment + * + */ + public void removeAllAlignment() + { + _alignmentList.removeAllElements(); + } //-- void removeAllAlignment() + + /** + * Method removeAllSequence + * + */ + public void removeAllSequence() + { + _sequenceList.removeAllElements(); + } //-- void removeAllSequence() + + /** + * Method removeAllSequenceSetAnnotations + * + */ + public void removeAllSequenceSetAnnotations() + { + _sequenceSetAnnotationsList.removeAllElements(); + } //-- void removeAllSequenceSetAnnotations() + + /** + * Method removeSequence + * + * + * + * @param index + * @return Sequence + */ + public org.vamsas.client.objects.Sequence removeSequence(int index) + { + java.lang.Object obj = _sequenceList.elementAt(index); + _sequenceList.removeElementAt(index); + return (org.vamsas.client.objects.Sequence) obj; + } //-- org.vamsas.client.objects.Sequence removeSequence(int) + + /** + * Method removeSequenceSetAnnotations + * + * + * + * @param index + * @return SequenceSetAnnotations + */ + public org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int index) + { + java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index); + _sequenceSetAnnotationsList.removeElementAt(index); + return (org.vamsas.client.objects.SequenceSetAnnotations) obj; + } //-- org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int) + + /** + * Sets the value of field 'aligned'. + * + * @param aligned the value of field 'aligned'. + */ + public void setAligned(boolean aligned) + { + this._aligned = aligned; + this._has_aligned = true; + } //-- void setAligned(boolean) + + /** + * Method setAlignment + * + * + * + * @param index + * @param vAlignment + */ + public void setAlignment(int index, org.vamsas.client.objects.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentList.size())) { + throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); + } + _alignmentList.setElementAt(vAlignment, index); + } //-- void setAlignment(int, org.vamsas.client.objects.Alignment) + + /** + * Method setAlignment + * + * + * + * @param alignmentArray + */ + public void setAlignment(org.vamsas.client.objects.Alignment[] alignmentArray) + { + //-- copy array + _alignmentList.removeAllElements(); + for (int i = 0; i < alignmentArray.length; i++) { + _alignmentList.addElement(alignmentArray[i]); + } + } //-- void setAlignment(org.vamsas.client.objects.Alignment) + + /** + * Method setAlignment + * + * Sets the value of 'alignment' by copying the given Vector. + * + * @param alignmentVector the Vector to copy. + */ + public void setAlignment(java.util.Vector alignmentVector) + { + //-- copy vector + _alignmentList.removeAllElements(); + for (int i = 0; i < alignmentVector.size(); i++) { + _alignmentList.addElement((org.vamsas.client.objects.Alignment)alignmentVector.elementAt(i)); + } + } //-- void setAlignment(java.util.Vector) + + /** + * Method setAlignmentAsReference + * + * Sets the value of 'alignment' by setting it to the given + * Vector. No type checking is performed. + * + * @param alignmentVector the Vector to copy. + */ + public void setAlignmentAsReference(java.util.Vector alignmentVector) + { + _alignmentList = alignmentVector; + } //-- void setAlignmentAsReference(java.util.Vector) + + /** + * Sets the value of field 'gapChar'. + * + * @param gapChar the value of field 'gapChar'. + */ + public void setGapChar(java.lang.String gapChar) + { + this._gapChar = gapChar; + } //-- void setGapChar(java.lang.String) + + /** + * Sets the value of field 'provenance'. + * + * @param provenance the value of field 'provenance'. + */ + public void setProvenance(org.vamsas.client.objects.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.client.objects.Provenance) + + /** + * Method setSequence + * + * + * + * @param index + * @param vSequence + */ + public void setSequence(int index, org.vamsas.client.objects.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceList.size())) { + throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); + } + _sequenceList.setElementAt(vSequence, index); + } //-- void setSequence(int, org.vamsas.client.objects.Sequence) + + /** + * Method setSequence + * + * + * + * @param sequenceArray + */ + public void setSequence(org.vamsas.client.objects.Sequence[] sequenceArray) + { + //-- copy array + _sequenceList.removeAllElements(); + for (int i = 0; i < sequenceArray.length; i++) { + _sequenceList.addElement(sequenceArray[i]); + } + } //-- void setSequence(org.vamsas.client.objects.Sequence) + + /** + * Method setSequence + * + * Sets the value of 'sequence' by copying the given Vector. + * + * @param sequenceVector the Vector to copy. + */ + public void setSequence(java.util.Vector sequenceVector) + { + //-- copy vector + _sequenceList.removeAllElements(); + for (int i = 0; i < sequenceVector.size(); i++) { + _sequenceList.addElement((org.vamsas.client.objects.Sequence)sequenceVector.elementAt(i)); + } + } //-- void setSequence(java.util.Vector) + + /** + * Method setSequenceAsReference + * + * Sets the value of 'sequence' by setting it to the given + * Vector. No type checking is performed. + * + * @param sequenceVector the Vector to copy. + */ + public void setSequenceAsReference(java.util.Vector sequenceVector) + { + _sequenceList = sequenceVector; + } //-- void setSequenceAsReference(java.util.Vector) + + /** + * Method setSequenceSetAnnotations + * + * + * + * @param index + * @param vSequenceSetAnnotations + */ + public void setSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) { + throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]"); + } + _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index); + } //-- void setSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations) + + /** + * Method setSequenceSetAnnotations + * + * + * + * @param sequenceSetAnnotationsArray + */ + public void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations[] sequenceSetAnnotationsArray) + { + //-- copy array + _sequenceSetAnnotationsList.removeAllElements(); + for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) { + _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]); + } + } //-- void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations) + + /** + * Method setSequenceSetAnnotations + * + * Sets the value of 'sequenceSetAnnotations' by copying the + * given Vector. + * + * @param sequenceSetAnnotationsVector the Vector to copy. + */ + public void setSequenceSetAnnotations(java.util.Vector sequenceSetAnnotationsVector) + { + //-- copy vector + _sequenceSetAnnotationsList.removeAllElements(); + for (int i = 0; i < sequenceSetAnnotationsVector.size(); i++) { + _sequenceSetAnnotationsList.addElement((org.vamsas.client.objects.SequenceSetAnnotations)sequenceSetAnnotationsVector.elementAt(i)); + } + } //-- void setSequenceSetAnnotations(java.util.Vector) + + /** + * Method setSequenceSetAnnotationsAsReference + * + * Sets the value of 'sequenceSetAnnotations' by setting it to + * the given Vector. No type checking is performed. + * + * @param sequenceSetAnnotationsVector the Vector to copy. + */ + public void setSequenceSetAnnotationsAsReference(java.util.Vector sequenceSetAnnotationsVector) + { + _sequenceSetAnnotationsList = sequenceSetAnnotationsVector; + } //-- void setSequenceSetAnnotationsAsReference(java.util.Vector) + + /** + * Sets the value of field 'tree'. + * + * @param tree the value of field 'tree'. + */ + public void setTree(org.vamsas.client.objects.Tree tree) + { + this._tree = tree; + } //-- void setTree(org.vamsas.client.objects.Tree) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return SequenceSet + */ + public static org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.SequenceSet) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSet.class, reader); + } //-- org.vamsas.client.objects.SequenceSet 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/client/objects/SequenceSetAnnotations.java b/src/org/vamsas/client/objects/SequenceSetAnnotations.java new file mode 100644 index 0000000..c9a124c --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceSetAnnotations.java @@ -0,0 +1,581 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceSetAnnotations. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetAnnotations extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _type + */ + private java.lang.String _type; + + /** + * Field _end + */ + private java.lang.String _end; + + /** + * Field _begin + */ + private java.lang.String _begin; + + /** + * Field _seqRef + */ + private java.lang.Object _seqRef; + + /** + * Field _description + */ + private java.lang.String _description; + + /** + * Field _status + */ + private java.lang.String _status; + + /** + * Field _annotationElementList + */ + private java.util.Vector _annotationElementList; + + /** + * Field _provenance + */ + private org.vamsas.client.objects.Provenance _provenance; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetAnnotations() + { + super(); + _annotationElementList = new Vector(); + } //-- org.vamsas.client.objects.SequenceSetAnnotations() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAnnotationElement + * + * + * + * @param vAnnotationElement + */ + public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + _annotationElementList.addElement(vAnnotationElement); + } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement) + + /** + * Method addAnnotationElement + * + * + * + * @param index + * @param vAnnotationElement + */ + public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + _annotationElementList.insertElementAt(vAnnotationElement, index); + } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) + + /** + * Method enumerateAnnotationElement + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAnnotationElement() + { + return _annotationElementList.elements(); + } //-- java.util.Enumeration enumerateAnnotationElement() + + /** + * 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 SequenceSetAnnotations) { + + SequenceSetAnnotations temp = (SequenceSetAnnotations)obj; + if (this._type != null) { + if (temp._type == null) return false; + else if (!(this._type.equals(temp._type))) + return false; + } + else if (temp._type != null) + return false; + if (this._end != null) { + if (temp._end == null) return false; + else if (!(this._end.equals(temp._end))) + return false; + } + else if (temp._end != null) + return false; + if (this._begin != null) { + if (temp._begin == null) return false; + else if (!(this._begin.equals(temp._begin))) + return false; + } + else if (temp._begin != null) + return false; + if (this._seqRef != null) { + if (temp._seqRef == null) return false; + else if (!(this._seqRef.equals(temp._seqRef))) + return false; + } + else if (temp._seqRef != null) + return false; + if (this._description != null) { + if (temp._description == null) return false; + else if (!(this._description.equals(temp._description))) + return false; + } + else if (temp._description != null) + return false; + if (this._status != null) { + if (temp._status == null) return false; + else if (!(this._status.equals(temp._status))) + return false; + } + else if (temp._status != null) + return false; + if (this._annotationElementList != null) { + if (temp._annotationElementList == null) return false; + else if (!(this._annotationElementList.equals(temp._annotationElementList))) + return false; + } + else if (temp._annotationElementList != 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) + + /** + * Method getAnnotationElement + * + * + * + * @param index + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationElementList.size())) { + throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + } + + return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); + } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int) + + /** + * Method getAnnotationElement + * + * + * + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() + { + int size = _annotationElementList.size(); + org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement() + + /** + * Method getAnnotationElementAsReference + * + * Returns a reference to 'annotationElement'. No type checking + * is performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getAnnotationElementAsReference() + { + return _annotationElementList; + } //-- java.util.Vector getAnnotationElementAsReference() + + /** + * Method getAnnotationElementCount + * + * + * + * @return int + */ + public int getAnnotationElementCount() + { + return _annotationElementList.size(); + } //-- int getAnnotationElementCount() + + /** + * Returns the value of field 'begin'. + * + * @return String + * @return the value of field 'begin'. + */ + public java.lang.String getBegin() + { + return this._begin; + } //-- java.lang.String getBegin() + + /** + * Returns the value of field 'description'. + * + * @return String + * @return the value of field 'description'. + */ + public java.lang.String getDescription() + { + return this._description; + } //-- java.lang.String getDescription() + + /** + * Returns the value of field 'end'. + * + * @return String + * @return the value of field 'end'. + */ + public java.lang.String getEnd() + { + return this._end; + } //-- java.lang.String getEnd() + + /** + * Returns the value of field 'provenance'. + * + * @return Provenance + * @return the value of field 'provenance'. + */ + public org.vamsas.client.objects.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.client.objects.Provenance getProvenance() + + /** + * Returns the value of field 'seqRef'. + * + * @return Object + * @return the value of field 'seqRef'. + */ + public java.lang.Object getSeqRef() + { + return this._seqRef; + } //-- java.lang.Object getSeqRef() + + /** + * Returns the value of field 'status'. + * + * @return String + * @return the value of field 'status'. + */ + public java.lang.String getStatus() + { + return this._status; + } //-- java.lang.String getStatus() + + /** + * Returns the value of field 'type'. + * + * @return String + * @return the value of field 'type'. + */ + public java.lang.String getType() + { + return this._type; + } //-- java.lang.String getType() + + /** + * 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 removeAllAnnotationElement + * + */ + public void removeAllAnnotationElement() + { + _annotationElementList.removeAllElements(); + } //-- void removeAllAnnotationElement() + + /** + * Method removeAnnotationElement + * + * + * + * @param index + * @return AnnotationElement + */ + public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index) + { + java.lang.Object obj = _annotationElementList.elementAt(index); + _annotationElementList.removeElementAt(index); + return (org.vamsas.client.objects.AnnotationElement) obj; + } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int) + + /** + * Method setAnnotationElement + * + * + * + * @param index + * @param vAnnotationElement + */ + public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationElementList.size())) { + throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); + } + _annotationElementList.setElementAt(vAnnotationElement, index); + } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement) + + /** + * Method setAnnotationElement + * + * + * + * @param annotationElementArray + */ + public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray) + { + //-- copy array + _annotationElementList.removeAllElements(); + for (int i = 0; i < annotationElementArray.length; i++) { + _annotationElementList.addElement(annotationElementArray[i]); + } + } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement) + + /** + * Method setAnnotationElement + * + * Sets the value of 'annotationElement' by copying the given + * Vector. + * + * @param annotationElementVector the Vector to copy. + */ + public void setAnnotationElement(java.util.Vector annotationElementVector) + { + //-- copy vector + _annotationElementList.removeAllElements(); + for (int i = 0; i < annotationElementVector.size(); i++) { + _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i)); + } + } //-- void setAnnotationElement(java.util.Vector) + + /** + * Method setAnnotationElementAsReference + * + * Sets the value of 'annotationElement' by setting it to the + * given Vector. No type checking is performed. + * + * @param annotationElementVector the Vector to copy. + */ + public void setAnnotationElementAsReference(java.util.Vector annotationElementVector) + { + _annotationElementList = annotationElementVector; + } //-- void setAnnotationElementAsReference(java.util.Vector) + + /** + * Sets the value of field 'begin'. + * + * @param begin the value of field 'begin'. + */ + public void setBegin(java.lang.String begin) + { + this._begin = begin; + } //-- void setBegin(java.lang.String) + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription(java.lang.String description) + { + this._description = description; + } //-- void setDescription(java.lang.String) + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd(java.lang.String end) + { + this._end = end; + } //-- void setEnd(java.lang.String) + + /** + * Sets the value of field 'provenance'. + * + * @param provenance the value of field 'provenance'. + */ + public void setProvenance(org.vamsas.client.objects.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.client.objects.Provenance) + + /** + * Sets the value of field 'seqRef'. + * + * @param seqRef the value of field 'seqRef'. + */ + public void setSeqRef(java.lang.Object seqRef) + { + this._seqRef = seqRef; + } //-- void setSeqRef(java.lang.Object) + + /** + * Sets the value of field 'status'. + * + * @param status the value of field 'status'. + */ + public void setStatus(java.lang.String status) + { + this._status = status; + } //-- void setStatus(java.lang.String) + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType(java.lang.String type) + { + this._type = type; + } //-- void setType(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return SequenceSetAnnotations + */ + public static org.vamsas.client.objects.SequenceSetAnnotations unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.SequenceSetAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSetAnnotations.class, reader); + } //-- org.vamsas.client.objects.SequenceSetAnnotations 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/client/objects/SequenceSetAnnotationsDescriptor.java b/src/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java new file mode 100644 index 0000000..91db452 --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceSetAnnotationsDescriptor.java @@ -0,0 +1,474 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceSetAnnotationsDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetAnnotationsDescriptor 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 SequenceSetAnnotationsDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "SequenceSetAnnotations"; + + //-- 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 + + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setType( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getEnd(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setEnd( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + 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); + //-- _begin + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getBegin(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setBegin( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _begin + 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); + //-- _seqRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setReference(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getSeqRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setSeqRef( (java.lang.Object) 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(); + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _seqRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setDescription( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _status + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getStatus(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setStatus( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _status + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _annotationElementList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getAnnotationElement(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.AnnotationElement(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationElementList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _provenance + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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 + { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + return target.getProvenance(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetAnnotations target = (SequenceSetAnnotations) object; + target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.SequenceSetAnnotationsDescriptor() + + + //-----------/ + //- 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.client.objects.SequenceSetAnnotations.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/client/objects/SequenceSetDescriptor.java b/src/org/vamsas/client/objects/SequenceSetDescriptor.java new file mode 100644 index 0000000..b193356 --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceSetDescriptor.java @@ -0,0 +1,433 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceSetDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetDescriptor 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 SequenceSetDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "SequenceSet"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _gapChar + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getGapChar(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setGapChar( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _gapChar + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _aligned + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + if(!target.hasAligned()) + return null; + return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAligned(); + return; + } + target.setAligned( ((java.lang.Boolean)value).booleanValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _aligned + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + BooleanValidator typeValidator = new BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequenceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequence( (org.vamsas.client.objects.Sequence) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _sequenceSetAnnotationsList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequenceSetAnnotations(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequenceSetAnnotations( (org.vamsas.client.objects.SequenceSetAnnotations) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.SequenceSetAnnotations(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetAnnotationsList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _alignmentList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAlignment(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addAlignment( (org.vamsas.client.objects.Alignment) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Alignment(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alignmentList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _tree + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_tree", "tree", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setTree( (org.vamsas.client.objects.Tree) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.Tree(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _tree + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _provenance + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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 + { + SequenceSet target = (SequenceSet) object; + return target.getProvenance(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.SequenceSetDescriptor() + + + //-----------/ + //- 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.client.objects.SequenceSet.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/client/objects/SequenceType.java b/src/org/vamsas/client/objects/SequenceType.java new file mode 100644 index 0000000..614f520 --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceType.java @@ -0,0 +1,529 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceType. + * + * @version $Revision$ $Date$ + */ +public class SequenceType extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _sequence + */ + private java.lang.String _sequence; + + /** + * Field _name + */ + private java.lang.String _name; + + /** + * Field _dbRefList + */ + private java.util.Vector _dbRefList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceType() + { + super(); + _dbRefList = new Vector(); + } //-- org.vamsas.client.objects.SequenceType() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addDbRef + * + * + * + * @param vDbRef + */ + public void addDbRef(org.vamsas.client.objects.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + _dbRefList.addElement(vDbRef); + } //-- void addDbRef(org.vamsas.client.objects.DbRef) + + /** + * Method addDbRef + * + * + * + * @param index + * @param vDbRef + */ + public void addDbRef(int index, org.vamsas.client.objects.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + _dbRefList.insertElementAt(vDbRef, index); + } //-- void addDbRef(int, org.vamsas.client.objects.DbRef) + + /** + * Method deleteEnd + * + */ + public void deleteEnd() + { + this._has_end= false; + } //-- void deleteEnd() + + /** + * Method deleteStart + * + */ + public void deleteStart() + { + this._has_start= false; + } //-- void deleteStart() + + /** + * Method enumerateDbRef + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateDbRef() + { + return _dbRefList.elements(); + } //-- java.util.Enumeration enumerateDbRef() + + /** + * 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 SequenceType) { + + SequenceType temp = (SequenceType)obj; + if (this._start != temp._start) + return false; + if (this._has_start != temp._has_start) + return false; + if (this._end != temp._end) + return false; + if (this._has_end != temp._has_end) + return false; + if (this._sequence != null) { + if (temp._sequence == null) return false; + else if (!(this._sequence.equals(temp._sequence))) + return false; + } + else if (temp._sequence != null) + return false; + if (this._name != null) { + if (temp._name == null) return false; + else if (!(this._name.equals(temp._name))) + return false; + } + else if (temp._name != null) + return false; + if (this._dbRefList != null) { + if (temp._dbRefList == null) return false; + else if (!(this._dbRefList.equals(temp._dbRefList))) + return false; + } + else if (temp._dbRefList != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Method getDbRef + * + * + * + * @param index + * @return DbRef + */ + public org.vamsas.client.objects.DbRef getDbRef(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _dbRefList.size())) { + throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + } + + return (org.vamsas.client.objects.DbRef) _dbRefList.elementAt(index); + } //-- org.vamsas.client.objects.DbRef getDbRef(int) + + /** + * Method getDbRef + * + * + * + * @return DbRef + */ + public org.vamsas.client.objects.DbRef[] getDbRef() + { + int size = _dbRefList.size(); + org.vamsas.client.objects.DbRef[] mArray = new org.vamsas.client.objects.DbRef[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.DbRef) _dbRefList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.DbRef[] getDbRef() + + /** + * Method getDbRefAsReference + * + * Returns a reference to 'dbRef'. No type checking is + * performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getDbRefAsReference() + { + return _dbRefList; + } //-- java.util.Vector getDbRefAsReference() + + /** + * Method getDbRefCount + * + * + * + * @return int + */ + public int getDbRefCount() + { + return _dbRefList.size(); + } //-- int getDbRefCount() + + /** + * Returns the value of field 'end'. + * + * @return int + * @return the value of field 'end'. + */ + public int getEnd() + { + return this._end; + } //-- int getEnd() + + /** + * Returns the value of field 'name'. + * + * @return String + * @return the value of field 'name'. + */ + public java.lang.String getName() + { + return this._name; + } //-- java.lang.String getName() + + /** + * Returns the value of field 'sequence'. + * + * @return String + * @return the value of field 'sequence'. + */ + public java.lang.String getSequence() + { + return this._sequence; + } //-- java.lang.String getSequence() + + /** + * Returns the value of field 'start'. + * + * @return int + * @return the value of field 'start'. + */ + public int getStart() + { + return this._start; + } //-- int getStart() + + /** + * Method hasEnd + * + * + * + * @return boolean + */ + public boolean hasEnd() + { + return this._has_end; + } //-- boolean hasEnd() + + /** + * Method hasStart + * + * + * + * @return boolean + */ + public boolean hasStart() + { + return this._has_start; + } //-- boolean hasStart() + + /** + * 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 removeAllDbRef + * + */ + public void removeAllDbRef() + { + _dbRefList.removeAllElements(); + } //-- void removeAllDbRef() + + /** + * Method removeDbRef + * + * + * + * @param index + * @return DbRef + */ + public org.vamsas.client.objects.DbRef removeDbRef(int index) + { + java.lang.Object obj = _dbRefList.elementAt(index); + _dbRefList.removeElementAt(index); + return (org.vamsas.client.objects.DbRef) obj; + } //-- org.vamsas.client.objects.DbRef removeDbRef(int) + + /** + * Method setDbRef + * + * + * + * @param index + * @param vDbRef + */ + public void setDbRef(int index, org.vamsas.client.objects.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _dbRefList.size())) { + throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + } + _dbRefList.setElementAt(vDbRef, index); + } //-- void setDbRef(int, org.vamsas.client.objects.DbRef) + + /** + * Method setDbRef + * + * + * + * @param dbRefArray + */ + public void setDbRef(org.vamsas.client.objects.DbRef[] dbRefArray) + { + //-- copy array + _dbRefList.removeAllElements(); + for (int i = 0; i < dbRefArray.length; i++) { + _dbRefList.addElement(dbRefArray[i]); + } + } //-- void setDbRef(org.vamsas.client.objects.DbRef) + + /** + * Method setDbRef + * + * Sets the value of 'dbRef' by copying the given Vector. + * + * @param dbRefVector the Vector to copy. + */ + public void setDbRef(java.util.Vector dbRefVector) + { + //-- copy vector + _dbRefList.removeAllElements(); + for (int i = 0; i < dbRefVector.size(); i++) { + _dbRefList.addElement((org.vamsas.client.objects.DbRef)dbRefVector.elementAt(i)); + } + } //-- void setDbRef(java.util.Vector) + + /** + * Method setDbRefAsReference + * + * Sets the value of 'dbRef' by setting it to the given Vector. + * No type checking is performed. + * + * @param dbRefVector the Vector to copy. + */ + public void setDbRefAsReference(java.util.Vector dbRefVector) + { + _dbRefList = dbRefVector; + } //-- void setDbRefAsReference(java.util.Vector) + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd(int end) + { + this._end = end; + this._has_end = true; + } //-- void setEnd(int) + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName(java.lang.String name) + { + this._name = name; + } //-- void setName(java.lang.String) + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence(java.lang.String sequence) + { + this._sequence = sequence; + } //-- void setSequence(java.lang.String) + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart(int start) + { + this._start = start; + this._has_start = true; + } //-- void setStart(int) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return SequenceType + */ + public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.SequenceType) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceType.class, reader); + } //-- org.vamsas.client.objects.SequenceType 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/client/objects/SequenceTypeDescriptor.java b/src/org/vamsas/client/objects/SequenceTypeDescriptor.java new file mode 100644 index 0000000..13069ad --- /dev/null +++ b/src/org/vamsas/client/objects/SequenceTypeDescriptor.java @@ -0,0 +1,373 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 SequenceTypeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceTypeDescriptor 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 SequenceTypeDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "SequenceType"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + if(!target.hasStart()) + return null; + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + // ignore null values for non optional primitives + if (value == null) return; + + target.setStart( ((java.lang.Integer)value).intValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + IntegerValidator typeValidator= new IntegerValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + if(!target.hasEnd()) + return null; + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + // ignore null values for non optional primitives + if (value == null) return; + + target.setEnd( ((java.lang.Integer)value).intValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + IntegerValidator typeValidator= new IntegerValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setSequence( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequence + 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); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setName( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + 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); + //-- _dbRefList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getDbRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.addDbRef( (org.vamsas.client.objects.DbRef) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.DbRef(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _dbRefList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.SequenceTypeDescriptor() + + + //-----------/ + //- 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.client.objects.SequenceType.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/client/objects/Tree.java b/src/org/vamsas/client/objects/Tree.java new file mode 100644 index 0000000..6affb22 --- /dev/null +++ b/src/org/vamsas/client/objects/Tree.java @@ -0,0 +1,212 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 Tree. + * + * @version $Revision$ $Date$ + */ +public class Tree extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _provenance + */ + private org.vamsas.client.objects.Provenance _provenance; + + /** + * Field _newickFormat + */ + private java.lang.String _newickFormat; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Tree() + { + super(); + } //-- org.vamsas.client.objects.Tree() + + + //-----------/ + //- 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 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.client.objects.Provenance getProvenance() + { + return this._provenance; + } //-- org.vamsas.client.objects.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) + + /** + * 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.client.objects.Provenance provenance) + { + this._provenance = provenance; + } //-- void setProvenance(org.vamsas.client.objects.Provenance) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Tree + */ + public static org.vamsas.client.objects.Tree unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.Tree) Unmarshaller.unmarshal(org.vamsas.client.objects.Tree.class, reader); + } //-- org.vamsas.client.objects.Tree 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/client/objects/TreeDescriptor.java b/src/org/vamsas/client/objects/TreeDescriptor.java new file mode 100644 index 0000000..bc09a23 --- /dev/null +++ b/src/org/vamsas/client/objects/TreeDescriptor.java @@ -0,0 +1,250 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 TreeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class TreeDescriptor 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 TreeDescriptor() + { + super(); + 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.client.objects.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.client.objects.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.client.objects.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.client.objects.TreeDescriptor() + + + //-----------/ + //- 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.client.objects.Tree.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/client/objects/VAMSAS.java b/src/org/vamsas/client/objects/VAMSAS.java new file mode 100644 index 0000000..664568b --- /dev/null +++ b/src/org/vamsas/client/objects/VAMSAS.java @@ -0,0 +1,550 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 VAMSAS. + * + * @version $Revision$ $Date$ + */ +public class VAMSAS extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _treeList + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList + */ + private java.util.Vector _sequenceSetList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSAS() + { + super(); + _treeList = new Vector(); + _sequenceSetList = new Vector(); + } //-- org.vamsas.client.objects.VAMSAS() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addSequenceSet + * + * + * + * @param vSequenceSet + */ + public void addSequenceSet(org.vamsas.client.objects.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetList.addElement(vSequenceSet); + } //-- void addSequenceSet(org.vamsas.client.objects.SequenceSet) + + /** + * Method addSequenceSet + * + * + * + * @param index + * @param vSequenceSet + */ + public void addSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetList.insertElementAt(vSequenceSet, index); + } //-- void addSequenceSet(int, org.vamsas.client.objects.SequenceSet) + + /** + * Method addTree + * + * + * + * @param vTree + */ + public void addTree(java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.addElement(vTree); + } //-- void addTree(java.lang.String) + + /** + * Method addTree + * + * + * + * @param index + * @param vTree + */ + public void addTree(int index, java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.insertElementAt(vTree, index); + } //-- void addTree(int, java.lang.String) + + /** + * Method enumerateSequenceSet + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSequenceSet() + { + return _sequenceSetList.elements(); + } //-- java.util.Enumeration enumerateSequenceSet() + + /** + * Method enumerateTree + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateTree() + { + return _treeList.elements(); + } //-- java.util.Enumeration enumerateTree() + + /** + * 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 VAMSAS) { + + VAMSAS temp = (VAMSAS)obj; + if (this._treeList != null) { + if (temp._treeList == null) return false; + else if (!(this._treeList.equals(temp._treeList))) + return false; + } + else if (temp._treeList != null) + return false; + if (this._sequenceSetList != null) { + if (temp._sequenceSetList == null) return false; + else if (!(this._sequenceSetList.equals(temp._sequenceSetList))) + return false; + } + else if (temp._sequenceSetList != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Method getSequenceSet + * + * + * + * @param index + * @return SequenceSet + */ + public org.vamsas.client.objects.SequenceSet getSequenceSet(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()+ "]"); + } + + return (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index); + } //-- org.vamsas.client.objects.SequenceSet getSequenceSet(int) + + /** + * Method getSequenceSet + * + * + * + * @return SequenceSet + */ + public org.vamsas.client.objects.SequenceSet[] getSequenceSet() + { + int size = _sequenceSetList.size(); + org.vamsas.client.objects.SequenceSet[] mArray = new org.vamsas.client.objects.SequenceSet[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index); + } + return mArray; + } //-- org.vamsas.client.objects.SequenceSet[] getSequenceSet() + + /** + * Method getSequenceSetAsReference + * + * Returns a reference to 'sequenceSet'. No type checking is + * performed on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getSequenceSetAsReference() + { + return _sequenceSetList; + } //-- java.util.Vector getSequenceSetAsReference() + + /** + * Method getSequenceSetCount + * + * + * + * @return int + */ + public int getSequenceSetCount() + { + return _sequenceSetList.size(); + } //-- int getSequenceSetCount() + + /** + * Method getTree + * + * + * + * @param index + * @return String + */ + public java.lang.String getTree(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()+ "]"); + } + + return (String)_treeList.elementAt(index); + } //-- java.lang.String getTree(int) + + /** + * Method getTree + * + * + * + * @return String + */ + public java.lang.String[] getTree() + { + int size = _treeList.size(); + java.lang.String[] mArray = new java.lang.String[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (String)_treeList.elementAt(index); + } + return mArray; + } //-- java.lang.String[] getTree() + + /** + * Method getTreeAsReference + * + * Returns a reference to 'tree'. No type checking is performed + * on any modications to the Vector. + * + * @return Vector + * @return returns a reference to the Vector. + */ + public java.util.Vector getTreeAsReference() + { + return _treeList; + } //-- java.util.Vector getTreeAsReference() + + /** + * Method getTreeCount + * + * + * + * @return int + */ + public int getTreeCount() + { + return _treeList.size(); + } //-- int getTreeCount() + + /** + * 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 removeAllSequenceSet + * + */ + public void removeAllSequenceSet() + { + _sequenceSetList.removeAllElements(); + } //-- void removeAllSequenceSet() + + /** + * Method removeAllTree + * + */ + public void removeAllTree() + { + _treeList.removeAllElements(); + } //-- void removeAllTree() + + /** + * Method removeSequenceSet + * + * + * + * @param index + * @return SequenceSet + */ + public org.vamsas.client.objects.SequenceSet removeSequenceSet(int index) + { + java.lang.Object obj = _sequenceSetList.elementAt(index); + _sequenceSetList.removeElementAt(index); + return (org.vamsas.client.objects.SequenceSet) obj; + } //-- org.vamsas.client.objects.SequenceSet removeSequenceSet(int) + + /** + * Method removeTree + * + * + * + * @param index + * @return String + */ + public java.lang.String removeTree(int index) + { + java.lang.Object obj = _treeList.elementAt(index); + _treeList.removeElementAt(index); + return (String)obj; + } //-- java.lang.String removeTree(int) + + /** + * Method setSequenceSet + * + * + * + * @param index + * @param vSequenceSet + */ + public void setSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceSetList.size())) { + throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]"); + } + _sequenceSetList.setElementAt(vSequenceSet, index); + } //-- void setSequenceSet(int, org.vamsas.client.objects.SequenceSet) + + /** + * Method setSequenceSet + * + * + * + * @param sequenceSetArray + */ + public void setSequenceSet(org.vamsas.client.objects.SequenceSet[] sequenceSetArray) + { + //-- copy array + _sequenceSetList.removeAllElements(); + for (int i = 0; i < sequenceSetArray.length; i++) { + _sequenceSetList.addElement(sequenceSetArray[i]); + } + } //-- void setSequenceSet(org.vamsas.client.objects.SequenceSet) + + /** + * Method setSequenceSet + * + * Sets the value of 'sequenceSet' by copying the given Vector. + * + * @param sequenceSetVector the Vector to copy. + */ + public void setSequenceSet(java.util.Vector sequenceSetVector) + { + //-- copy vector + _sequenceSetList.removeAllElements(); + for (int i = 0; i < sequenceSetVector.size(); i++) { + _sequenceSetList.addElement((org.vamsas.client.objects.SequenceSet)sequenceSetVector.elementAt(i)); + } + } //-- void setSequenceSet(java.util.Vector) + + /** + * Method setSequenceSetAsReference + * + * Sets the value of 'sequenceSet' by setting it to the given + * Vector. No type checking is performed. + * + * @param sequenceSetVector the Vector to copy. + */ + public void setSequenceSetAsReference(java.util.Vector sequenceSetVector) + { + _sequenceSetList = sequenceSetVector; + } //-- void setSequenceSetAsReference(java.util.Vector) + + /** + * 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 setTree + * + * Sets the value of 'tree' by copying the given Vector. + * + * @param treeVector the Vector to copy. + */ + public void setTree(java.util.Vector treeVector) + { + //-- copy vector + _treeList.removeAllElements(); + for (int i = 0; i < treeVector.size(); i++) { + _treeList.addElement((java.lang.String)treeVector.elementAt(i)); + } + } //-- void setTree(java.util.Vector) + + /** + * Method setTreeAsReference + * + * Sets the value of 'tree' by setting it to the given Vector. + * No type checking is performed. + * + * @param treeVector the Vector to copy. + */ + public void setTreeAsReference(java.util.Vector treeVector) + { + _treeList = treeVector; + } //-- void setTreeAsReference(java.util.Vector) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return VAMSAS + */ + public static org.vamsas.client.objects.VAMSAS unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.client.objects.VAMSAS) Unmarshaller.unmarshal(org.vamsas.client.objects.VAMSAS.class, reader); + } //-- org.vamsas.client.objects.VAMSAS 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/client/objects/VAMSASDescriptor.java b/src/org/vamsas/client/objects/VAMSASDescriptor.java new file mode 100644 index 0000000..e3d896f --- /dev/null +++ b/src/org/vamsas/client/objects/VAMSASDescriptor.java @@ -0,0 +1,248 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M1, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.client.objects; + + //---------------------------------/ + //- 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 VAMSASDescriptor. + * + * @version $Revision$ $Date$ + */ +public class VAMSASDescriptor 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 VAMSASDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "VAMSAS"; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addTree( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + 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 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getSequenceSet(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addSequenceSet( (org.vamsas.client.objects.SequenceSet) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.client.objects.SequenceSet(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); + } //-- org.vamsas.client.objects.VAMSASDescriptor() + + + //-----------/ + //- 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.client.objects.VAMSAS.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() + +} -- 1.7.10.2