+++ /dev/null
--- listing properties --\r
-org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr...\r
-org.vamsas.objects.core.VamsasDocument=org.vamsas.objects.core.VamsasDocumen...\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Alignment.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Alignment.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class Alignment extends uk.ac.vamsas.client.Vobject
-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;
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable
- */
- private java.lang.String _modifiable;
-
- /**
- * This is annotation over the coordinate frame
- * defined by all the columns in the alignment.
- *
- */
- private java.util.Vector _alignmentAnnotationList;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _alignmentSequenceList
- */
- private java.util.Vector _alignmentSequenceList;
-
- /**
- * typical properties may be additional
- * alignment score objects
- */
- private java.util.Vector _propertyList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment()
- {
- super();
- _alignmentAnnotationList = new Vector();
- _treeList = new Vector();
- _alignmentSequenceList = new Vector();
- _propertyList = new Vector();
- } //-- org.vamsas.objects.core.Alignment()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignmentAnnotation
- *
- *
- *
- * @param vAlignmentAnnotation
- */
- public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentAnnotationList.addElement(vAlignmentAnnotation);
- } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method addAlignmentAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- */
- public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
- } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method addAlignmentSequence
- *
- *
- *
- * @param vAlignmentSequence
- */
- public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceList.addElement(vAlignmentSequence);
- } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
-
- /**
- * Method addAlignmentSequence
- *
- *
- *
- * @param index
- * @param vAlignmentSequence
- */
- public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
- } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, org.vamsas.objects.core.Tree)
-
- /**
- * Method deleteAligned
- *
- */
- public void deleteAligned()
- {
- this._has_aligned= false;
- } //-- void deleteAligned()
-
- /**
- * Method enumerateAlignmentAnnotation
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentAnnotation()
- {
- return _alignmentAnnotationList.elements();
- } //-- java.util.Enumeration enumerateAlignmentAnnotation()
-
- /**
- * Method enumerateAlignmentSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentSequence()
- {
- return _alignmentSequenceList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequence()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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._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._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- else if (!(this._modifiable.equals(temp._modifiable)))
- return false;
- }
- else if (temp._modifiable != null)
- return false;
- if (this._alignmentAnnotationList != null) {
- if (temp._alignmentAnnotationList == null) return false;
- else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
- return false;
- }
- else if (temp._alignmentAnnotationList != 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._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != 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 getAlignmentAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
-
- /**
- * Method getAlignmentAnnotation
- *
- *
- *
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
- {
- int size = _alignmentAnnotationList.size();
- org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
-
- /**
- * Method getAlignmentAnnotationCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentAnnotationCount()
- {
- return _alignmentAnnotationList.size();
- } //-- int getAlignmentAnnotationCount()
-
- /**
- * Method getAlignmentSequence
- *
- *
- *
- * @param index
- * @return AlignmentSequence
- */
- public org.vamsas.objects.core.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.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
-
- /**
- * Method getAlignmentSequence
- *
- *
- *
- * @return AlignmentSequence
- */
- public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
- {
- int size = _alignmentSequenceList.size();
- org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
-
- /**
- * Method getAlignmentSequenceCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentSequenceCount()
- {
- return _alignmentSequenceList.size();
- } //-- int getAlignmentSequenceCount()
-
- /**
- * 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 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return String
- * @return the value of field 'modifiable'.
- */
- public java.lang.String getModifiable()
- {
- return this._modifiable;
- } //-- java.lang.String getModifiable()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index);
- } //-- org.vamsas.objects.core.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public org.vamsas.objects.core.Tree[] getTree()
- {
- int size = _treeList.size();
- org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Tree[] getTree()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * 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 removeAlignmentAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
- {
- java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
- _alignmentAnnotationList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentAnnotation) obj;
- } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
-
- /**
- * Method removeAlignmentSequence
- *
- *
- *
- * @param index
- * @return AlignmentSequence
- */
- public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
- {
- java.lang.Object obj = _alignmentSequenceList.elementAt(index);
- _alignmentSequenceList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentSequence) obj;
- } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
-
- /**
- * Method removeAllAlignmentAnnotation
- *
- */
- public void removeAllAlignmentAnnotation()
- {
- _alignmentAnnotationList.removeAllElements();
- } //-- void removeAllAlignmentAnnotation()
-
- /**
- * Method removeAllAlignmentSequence
- *
- */
- public void removeAllAlignmentSequence()
- {
- _alignmentSequenceList.removeAllElements();
- } //-- void removeAllAlignmentSequence()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (org.vamsas.objects.core.Tree) obj;
- } //-- org.vamsas.objects.core.Tree removeTree(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 setAlignmentAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- */
- public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
- }
- _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
- } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method setAlignmentAnnotation
- *
- *
- *
- * @param alignmentAnnotationArray
- */
- public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
- {
- //-- copy array
- _alignmentAnnotationList.removeAllElements();
- for (int i = 0; i < alignmentAnnotationArray.length; i++) {
- _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
- }
- } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method setAlignmentSequence
- *
- *
- *
- * @param index
- * @param vAlignmentSequence
- */
- public void setAlignmentSequence(int index, org.vamsas.objects.core.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.objects.core.AlignmentSequence)
-
- /**
- * Method setAlignmentSequence
- *
- *
- *
- * @param alignmentSequenceArray
- */
- public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
- {
- //-- copy array
- _alignmentSequenceList.removeAllElements();
- for (int i = 0; i < alignmentSequenceArray.length; i++) {
- _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
- }
- } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
-
- /**
- * 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 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(java.lang.String modifiable)
- {
- this._modifiable = modifiable;
- } //-- void setModifiable(java.lang.String)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(org.vamsas.objects.core.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Alignment
- */
- public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
- } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * This is annotation over the coordinate frame\r
- * defined by all the columns in the alignment.\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _provenance\r
- */\r
- private org.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentAnnotation() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AlignmentAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AlignmentAnnotation) {\r
- \r
- AlignmentAnnotation temp = (AlignmentAnnotation)obj;\r
- if (this._graph != temp._graph)\r
- return false;\r
- if (this._has_graph != temp._has_graph)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
- }\r
- else if (temp._provenance != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return Provenance\r
- * @return the value of field 'provenance'.\r
- */\r
- public org.vamsas.objects.core.Provenance getProvenance()\r
- {\r
- return this._provenance;\r
- } //-- org.vamsas.objects.core.Provenance getProvenance() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'graph'. The field 'graph' has the\r
- * following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph)\r
- {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
-\r
- /**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)\r
- {\r
- this._provenance = provenance;\r
- } //-- void setProvenance(org.vamsas.objects.core.Provenance) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AlignmentAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "AlignmentAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _graph\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- if(!target.hasGraph())\r
- return null;\r
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setGraph( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _graph\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _provenance\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- return target.getProvenance();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Provenance();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _provenance\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AlignmentAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AlignmentAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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
-
- //-- _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
- {
- Alignment target = (Alignment) object;
- return target.getGapChar();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) 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
- {
- Alignment target = (Alignment) 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 {
- Alignment target = (Alignment) 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);
- //-- _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
- {
- Alignment target = (Alignment) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _modifiable
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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
- {
- Alignment target = (Alignment) object;
- return target.getModifiable();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.setModifiable( (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: _modifiable
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _alignmentAnnotationList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotation.class, "_alignmentAnnotationList", "AlignmentAnnotation", 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.getAlignmentAnnotation();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.addAlignmentAnnotation( (org.vamsas.objects.core.AlignmentAnnotation) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.AlignmentAnnotation();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignmentAnnotationList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- 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.objects.core.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.objects.core.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.objects.core.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.objects.core.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.objects.core.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(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alignment target = (Alignment) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.addProperty( (org.vamsas.objects.core.Property) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- 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.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class AlignmentSequence.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentSequence extends org.vamsas.objects.core.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object
- * referencing
- */
- private java.lang.String _id;
-
- /**
- * Dataset Sequence from which
- * this alignment sequence is taken from
- *
- */
- private java.lang.Object _refid;
-
- /**
- * Field _alignmentSequenceAnnotationList
- */
- private java.util.Vector _alignmentSequenceAnnotationList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlignmentSequence()
- {
- super();
- _alignmentSequenceAnnotationList = new Vector();
- } //-- org.vamsas.objects.core.AlignmentSequence()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignmentSequenceAnnotation
- *
- *
- *
- * @param vAlignmentSequenceAnnotation
- */
- public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
- } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method addAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentSequenceAnnotation
- */
- public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method enumerateAlignmentSequenceAnnotation
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
- {
- return _alignmentSequenceAnnotationList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
-
- /**
- * 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;
- if (this._refid != null) {
- if (temp._refid == null) return false;
- else if (!(this._refid.equals(temp._refid)))
- return false;
- }
- else if (temp._refid != null)
- return false;
- if (this._alignmentSequenceAnnotationList != null) {
- if (temp._alignmentSequenceAnnotationList == null) return false;
- else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
- return false;
- }
- else if (temp._alignmentSequenceAnnotationList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentSequenceAnnotation
- */
- public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
-
- /**
- * Method getAlignmentSequenceAnnotation
- *
- *
- *
- * @return AlignmentSequenceAnnotation
- */
- public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
- {
- int size = _alignmentSequenceAnnotationList.size();
- org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
-
- /**
- * Method getAlignmentSequenceAnnotationCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentSequenceAnnotationCount()
- {
- return _alignmentSequenceAnnotationList.size();
- } //-- int getAlignmentSequenceAnnotationCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'refid'. The field 'refid' has
- * the following description: Dataset Sequence from which
- * this alignment sequence is taken from
- *
- *
- * @return Object
- * @return the value of field 'refid'.
- */
- public java.lang.Object getRefid()
- {
- return this._refid;
- } //-- java.lang.Object getRefid()
-
- /**
- * 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 removeAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentSequenceAnnotation
- */
- public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
- {
- java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
- _alignmentSequenceAnnotationList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
-
- /**
- * Method removeAllAlignmentSequenceAnnotation
- *
- */
- public void removeAllAlignmentSequenceAnnotation()
- {
- _alignmentSequenceAnnotationList.removeAllElements();
- } //-- void removeAllAlignmentSequenceAnnotation()
-
- /**
- * Method setAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentSequenceAnnotation
- */
- public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
- }
- _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method setAlignmentSequenceAnnotation
- *
- *
- *
- * @param alignmentSequenceAnnotationArray
- */
- public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
- {
- //-- copy array
- _alignmentSequenceAnnotationList.removeAllElements();
- for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
- _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
- }
- } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'refid'. The field 'refid' has the
- * following description: Dataset Sequence from which
- * this alignment sequence is taken from
- *
- *
- * @param refid the value of field 'refid'.
- */
- public void setRefid(java.lang.Object refid)
- {
- this._refid = refid;
- } //-- void setRefid(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceType
- */
- public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader);
- } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class AlignmentSequenceAnnotation.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _provenance\r
- */\r
- private org.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentSequenceAnnotation() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AlignmentSequenceAnnotation) {\r
- \r
- AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;\r
- if (this._graph != temp._graph)\r
- return false;\r
- if (this._has_graph != temp._has_graph)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
- }\r
- else if (temp._provenance != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return Provenance\r
- * @return the value of field 'provenance'.\r
- */\r
- public org.vamsas.objects.core.Provenance getProvenance()\r
- {\r
- return this._provenance;\r
- } //-- org.vamsas.objects.core.Provenance getProvenance() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'graph'. The field 'graph' has the\r
- * following description: TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph)\r
- {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
-\r
- /**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)\r
- {\r
- this._provenance = provenance;\r
- } //-- void setProvenance(org.vamsas.objects.core.Provenance) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AlignmentSequenceAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentSequenceAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "AlignmentSequenceAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _graph\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- if(!target.hasGraph())\r
- return null;\r
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setGraph( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _graph\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _provenance\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- return target.getProvenance();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Provenance();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _provenance\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AlignmentSequenceAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class AlignmentSequenceDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.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.objects.core.SequenceTypeDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "alignmentSequence";
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- 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.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _refid
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute);
- desc.setReference(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlignmentSequence target = (AlignmentSequence) object;
- return target.getRefid();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentSequence target = (AlignmentSequence) object;
- target.setRefid( (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: _refid
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _alignmentSequenceAnnotationList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, "_alignmentSequenceAnnotationList", "AlignmentSequenceAnnotation", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlignmentSequence target = (AlignmentSequence) object;
- return target.getAlignmentSequenceAnnotation();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentSequence target = (AlignmentSequence) object;
- target.addAlignmentSequenceAnnotation( (org.vamsas.objects.core.AlignmentSequenceAnnotation) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.AlignmentSequenceAnnotation();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignmentSequenceAnnotationList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:AnnotationElement.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class AnnotationElement.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class AnnotationElement extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * position with respect to the coordinate frame defined by a
- * rangeType specification
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * true means the annotation element appears between the
- * specified position and the next
- */
- private boolean _after = false;
-
- /**
- * keeps track of state for field: _after
- */
- private boolean _has_after;
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Free text at this position
- */
- private java.lang.String _description;
-
- /**
- * Discrete symbol - possibly graphically represented
- *
- */
- private java.util.Vector _glyphList;
-
- /**
- * Ordered set of float values - an application may treat
- * the values together as a vector with common support for a
- * set of
- * annotation elements - but this is, again, not validated so
- * applications
- * should deal gracefully with varying numbers of dimensions
- *
- */
- private java.util.Vector _valueList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElement()
- {
- super();
- _glyphList = new Vector();
- _valueList = new Vector();
- } //-- org.vamsas.objects.core.AnnotationElement()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addGlyph
- *
- *
- *
- * @param vGlyph
- */
- public void addGlyph(org.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException
- {
- _glyphList.addElement(vGlyph);
- } //-- void addGlyph(org.vamsas.objects.core.Glyph)
-
- /**
- * Method addGlyph
- *
- *
- *
- * @param index
- * @param vGlyph
- */
- public void addGlyph(int index, org.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException
- {
- _glyphList.insertElementAt(vGlyph, index);
- } //-- void addGlyph(int, org.vamsas.objects.core.Glyph)
-
- /**
- * Method addValue
- *
- *
- *
- * @param vValue
- */
- public void addValue(float vValue)
- throws java.lang.IndexOutOfBoundsException
- {
- _valueList.addElement(new java.lang.Float(vValue));
- } //-- void addValue(float)
-
- /**
- * Method addValue
- *
- *
- *
- * @param index
- * @param vValue
- */
- public void addValue(int index, float vValue)
- throws java.lang.IndexOutOfBoundsException
- {
- _valueList.insertElementAt(new java.lang.Float(vValue), index);
- } //-- void addValue(int, float)
-
- /**
- * Method deleteAfter
- *
- */
- public void deleteAfter()
- {
- this._has_after= false;
- } //-- void deleteAfter()
-
- /**
- * Method deletePosition
- *
- */
- public void deletePosition()
- {
- this._has_position= false;
- } //-- void deletePosition()
-
- /**
- * Method enumerateGlyph
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateGlyph()
- {
- return _glyphList.elements();
- } //-- java.util.Enumeration enumerateGlyph()
-
- /**
- * Method enumerateValue
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateValue()
- {
- return _valueList.elements();
- } //-- java.util.Enumeration enumerateValue()
-
- /**
- * 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._after != temp._after)
- return false;
- if (this._has_after != temp._has_after)
- return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- return false;
- }
- else if (temp._description != null)
- return false;
- if (this._glyphList != null) {
- if (temp._glyphList == null) return false;
- else if (!(this._glyphList.equals(temp._glyphList)))
- return false;
- }
- else if (temp._glyphList != null)
- return false;
- if (this._valueList != null) {
- if (temp._valueList == null) return false;
- else if (!(this._valueList.equals(temp._valueList)))
- return false;
- }
- else if (temp._valueList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'after'. The field 'after' has
- * the following description: true means the annotation element
- * appears between the
- * specified position and the next
- *
- * @return boolean
- * @return the value of field 'after'.
- */
- public boolean getAfter()
- {
- return this._after;
- } //-- boolean getAfter()
-
- /**
- * Returns the value of field 'description'. The field
- * 'description' has the following description: Free text at
- * this position
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Method getGlyph
- *
- *
- *
- * @param index
- * @return Glyph
- */
- public org.vamsas.objects.core.Glyph getGlyph(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _glyphList.size())) {
- throw new IndexOutOfBoundsException("getGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
- } //-- org.vamsas.objects.core.Glyph getGlyph(int)
-
- /**
- * Method getGlyph
- *
- *
- *
- * @return Glyph
- */
- public org.vamsas.objects.core.Glyph[] getGlyph()
- {
- int size = _glyphList.size();
- org.vamsas.objects.core.Glyph[] mArray = new org.vamsas.objects.core.Glyph[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Glyph[] getGlyph()
-
- /**
- * Method getGlyphCount
- *
- *
- *
- * @return int
- */
- public int getGlyphCount()
- {
- return _glyphList.size();
- } //-- int getGlyphCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'position'. The field 'position'
- * has the following description: position with respect to the
- * coordinate frame defined by a
- * rangeType specification
- *
- * @return int
- * @return the value of field 'position'.
- */
- public int getPosition()
- {
- return this._position;
- } //-- int getPosition()
-
- /**
- * Method getValue
- *
- *
- *
- * @param index
- * @return float
- */
- public float getValue(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _valueList.size())) {
- throw new IndexOutOfBoundsException("getValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]");
- }
-
- return ((java.lang.Float)_valueList.elementAt(index)).floatValue();
- } //-- float getValue(int)
-
- /**
- * Method getValue
- *
- *
- *
- * @return float
- */
- public float[] getValue()
- {
- int size = _valueList.size();
- float[] mArray = new float[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = ((java.lang.Float)_valueList.elementAt(index)).floatValue();
- }
- return mArray;
- } //-- float[] getValue()
-
- /**
- * Method getValueCount
- *
- *
- *
- * @return int
- */
- public int getValueCount()
- {
- return _valueList.size();
- } //-- int getValueCount()
-
- /**
- * Method hasAfter
- *
- *
- *
- * @return boolean
- */
- public boolean hasAfter()
- {
- return this._has_after;
- } //-- boolean hasAfter()
-
- /**
- * Method hasPosition
- *
- *
- *
- * @return boolean
- */
- public boolean hasPosition()
- {
- return this._has_position;
- } //-- boolean hasPosition()
-
- /**
- * 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 removeAllGlyph
- *
- */
- public void removeAllGlyph()
- {
- _glyphList.removeAllElements();
- } //-- void removeAllGlyph()
-
- /**
- * Method removeAllValue
- *
- */
- public void removeAllValue()
- {
- _valueList.removeAllElements();
- } //-- void removeAllValue()
-
- /**
- * Method removeGlyph
- *
- *
- *
- * @param index
- * @return Glyph
- */
- public org.vamsas.objects.core.Glyph removeGlyph(int index)
- {
- java.lang.Object obj = _glyphList.elementAt(index);
- _glyphList.removeElementAt(index);
- return (org.vamsas.objects.core.Glyph) obj;
- } //-- org.vamsas.objects.core.Glyph removeGlyph(int)
-
- /**
- * Method removeValue
- *
- *
- *
- * @param index
- * @return float
- */
- public float removeValue(int index)
- {
- java.lang.Object obj = _valueList.elementAt(index);
- _valueList.removeElementAt(index);
- return ((java.lang.Float)obj).floatValue();
- } //-- float removeValue(int)
-
- /**
- * Sets the value of field 'after'. The field 'after' has the
- * following description: true means the annotation element
- * appears between the
- * specified position and the next
- *
- * @param after the value of field 'after'.
- */
- public void setAfter(boolean after)
- {
- this._after = after;
- this._has_after = true;
- } //-- void setAfter(boolean)
-
- /**
- * Sets the value of field 'description'. The field
- * 'description' has the following description: Free text at
- * this position
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Method setGlyph
- *
- *
- *
- * @param index
- * @param vGlyph
- */
- public void setGlyph(int index, org.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _glyphList.size())) {
- throw new IndexOutOfBoundsException("setGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]");
- }
- _glyphList.setElementAt(vGlyph, index);
- } //-- void setGlyph(int, org.vamsas.objects.core.Glyph)
-
- /**
- * Method setGlyph
- *
- *
- *
- * @param glyphArray
- */
- public void setGlyph(org.vamsas.objects.core.Glyph[] glyphArray)
- {
- //-- copy array
- _glyphList.removeAllElements();
- for (int i = 0; i < glyphArray.length; i++) {
- _glyphList.addElement(glyphArray[i]);
- }
- } //-- void setGlyph(org.vamsas.objects.core.Glyph)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'position'. The field 'position' has
- * the following description: position with respect to the
- * coordinate frame defined by a
- * rangeType specification
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(int position)
- {
- this._position = position;
- this._has_position = true;
- } //-- void setPosition(int)
-
- /**
- * Method setValue
- *
- *
- *
- * @param index
- * @param vValue
- */
- public void setValue(int index, float vValue)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _valueList.size())) {
- throw new IndexOutOfBoundsException("setValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]");
- }
- _valueList.setElementAt(new java.lang.Float(vValue), index);
- } //-- void setValue(int, float)
-
- /**
- * Method setValue
- *
- *
- *
- * @param valueArray
- */
- public void setValue(float[] valueArray)
- {
- //-- copy array
- _valueList.removeAllElements();
- for (int i = 0; i < valueArray.length; i++) {
- _valueList.addElement(new java.lang.Float(valueArray[i]));
- }
- } //-- void setValue(float)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return AnnotationElement
- */
- public static org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader);
- } //-- org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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);
- //-- _after
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_after", "after", 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.hasAfter())
- return null;
- return (target.getAfter() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAfter();
- return;
- }
- target.setAfter( ((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: _after
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- BooleanValidator typeValidator = new BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _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.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);
- //-- _glyphList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Glyph.class, "_glyphList", "glyph", 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;
- return target.getGlyph();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.addGlyph( (org.vamsas.objects.core.Glyph) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Glyph();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _glyphList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _valueList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_valueList", "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;
- return 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.addValue( ((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.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _valueList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- FloatValidator typeValidator = new FloatValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class AppData.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AppData extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Internal choice value storage\r
- */\r
- private java.lang.Object _choiceValue;\r
-\r
- /**\r
- * Field _data\r
- */\r
- private byte[] _data;\r
-\r
- /**\r
- * Field _dataReference\r
- */\r
- private java.lang.String _dataReference;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AppData() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AppData()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AppData) {\r
- \r
- AppData temp = (AppData)obj;\r
- if (this._choiceValue != null) {\r
- if (temp._choiceValue == null) return false;\r
- else if (!(this._choiceValue.equals(temp._choiceValue))) \r
- return false;\r
- }\r
- else if (temp._choiceValue != null)\r
- return false;\r
- if (this._data != null) {\r
- if (temp._data == null) return false;\r
- else if (!(this._data.equals(temp._data))) \r
- return false;\r
- }\r
- else if (temp._data != null)\r
- return false;\r
- if (this._dataReference != null) {\r
- if (temp._dataReference == null) return false;\r
- else if (!(this._dataReference.equals(temp._dataReference))) \r
- return false;\r
- }\r
- else if (temp._dataReference != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'choiceValue'. The field\r
- * 'choiceValue' has the following description: Internal choice\r
- * value storage\r
- * \r
- * @return Object\r
- * @return the value of field 'choiceValue'.\r
- */\r
- public java.lang.Object getChoiceValue()\r
- {\r
- return this._choiceValue;\r
- } //-- java.lang.Object getChoiceValue() \r
-\r
- /**\r
- * Returns the value of field 'data'.\r
- * \r
- * @return byte\r
- * @return the value of field 'data'.\r
- */\r
- public byte[] getData()\r
- {\r
- return this._data;\r
- } //-- byte[] getData() \r
-\r
- /**\r
- * Returns the value of field 'dataReference'.\r
- * \r
- * @return String\r
- * @return the value of field 'dataReference'.\r
- */\r
- public java.lang.String getDataReference()\r
- {\r
- return this._dataReference;\r
- } //-- java.lang.String getDataReference() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'data'.\r
- * \r
- * @param data the value of field 'data'.\r
- */\r
- public void setData(byte[] data)\r
- {\r
- this._data = data;\r
- this._choiceValue = data;\r
- } //-- void setData(byte) \r
-\r
- /**\r
- * Sets the value of field 'dataReference'.\r
- * \r
- * @param dataReference the value of field 'dataReference'.\r
- */\r
- public void setDataReference(java.lang.String dataReference)\r
- {\r
- this._dataReference = dataReference;\r
- this._choiceValue = dataReference;\r
- } //-- void setDataReference(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AppData) Unmarshaller.unmarshal(org.vamsas.objects.core.AppData.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AppDataDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AppDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AppDataDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "appData";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- initialize element descriptors\r
- \r
- //-- _data\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(byte[].class, "_data", "data", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AppData target = (AppData) object;\r
- return target.getData();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AppData target = (AppData) object;\r
- target.setData( (byte[]) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _data\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _dataReference\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dataReference", "dataReference", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AppData target = (AppData) object;\r
- return target.getDataReference();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AppData target = (AppData) object;\r
- target.setDataReference( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _dataReference\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AppDataDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AppData.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class ApplicationData.
- *
- * @version $Revision$ $Date$
- */
-public class ApplicationData extends org.vamsas.objects.core.AppData
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Version string describing the application specific
- * data storage version used
- */
- private java.lang.String _version;
-
- /**
- * Canonical name of application
- */
- private java.lang.String _name;
-
- /**
- * Field _userList
- */
- private java.util.Vector _userList;
-
- /**
- * Field _common
- */
- private org.vamsas.objects.core.Common _common;
-
- /**
- * Field _instanceList
- */
- private java.util.Vector _instanceList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ApplicationData()
- {
- super();
- _userList = new Vector();
- _instanceList = new Vector();
- } //-- org.vamsas.objects.core.ApplicationData()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addInstance
- *
- *
- *
- * @param vInstance
- */
- public void addInstance(org.vamsas.objects.core.Instance vInstance)
- throws java.lang.IndexOutOfBoundsException
- {
- _instanceList.addElement(vInstance);
- } //-- void addInstance(org.vamsas.objects.core.Instance)
-
- /**
- * Method addInstance
- *
- *
- *
- * @param index
- * @param vInstance
- */
- public void addInstance(int index, org.vamsas.objects.core.Instance vInstance)
- throws java.lang.IndexOutOfBoundsException
- {
- _instanceList.insertElementAt(vInstance, index);
- } //-- void addInstance(int, org.vamsas.objects.core.Instance)
-
- /**
- * Method addUser
- *
- *
- *
- * @param vUser
- */
- public void addUser(org.vamsas.objects.core.User vUser)
- throws java.lang.IndexOutOfBoundsException
- {
- _userList.addElement(vUser);
- } //-- void addUser(org.vamsas.objects.core.User)
-
- /**
- * Method addUser
- *
- *
- *
- * @param index
- * @param vUser
- */
- public void addUser(int index, org.vamsas.objects.core.User vUser)
- throws java.lang.IndexOutOfBoundsException
- {
- _userList.insertElementAt(vUser, index);
- } //-- void addUser(int, org.vamsas.objects.core.User)
-
- /**
- * Method enumerateInstance
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateInstance()
- {
- return _instanceList.elements();
- } //-- java.util.Enumeration enumerateInstance()
-
- /**
- * Method enumerateUser
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateUser()
- {
- return _userList.elements();
- } //-- java.util.Enumeration enumerateUser()
-
- /**
- * 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._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;
- if (this._userList != null) {
- if (temp._userList == null) return false;
- else if (!(this._userList.equals(temp._userList)))
- return false;
- }
- else if (temp._userList != null)
- return false;
- if (this._common != null) {
- if (temp._common == null) return false;
- else if (!(this._common.equals(temp._common)))
- return false;
- }
- else if (temp._common != null)
- return false;
- if (this._instanceList != null) {
- if (temp._instanceList == null) return false;
- else if (!(this._instanceList.equals(temp._instanceList)))
- return false;
- }
- else if (temp._instanceList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'common'.
- *
- * @return Common
- * @return the value of field 'common'.
- */
- public org.vamsas.objects.core.Common getCommon()
- {
- return this._common;
- } //-- org.vamsas.objects.core.Common getCommon()
-
- /**
- * Method getInstance
- *
- *
- *
- * @param index
- * @return Instance
- */
- public org.vamsas.objects.core.Instance getInstance(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _instanceList.size())) {
- throw new IndexOutOfBoundsException("getInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Instance) _instanceList.elementAt(index);
- } //-- org.vamsas.objects.core.Instance getInstance(int)
-
- /**
- * Method getInstance
- *
- *
- *
- * @return Instance
- */
- public org.vamsas.objects.core.Instance[] getInstance()
- {
- int size = _instanceList.size();
- org.vamsas.objects.core.Instance[] mArray = new org.vamsas.objects.core.Instance[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Instance) _instanceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Instance[] getInstance()
-
- /**
- * Method getInstanceCount
- *
- *
- *
- * @return int
- */
- public int getInstanceCount()
- {
- return _instanceList.size();
- } //-- int getInstanceCount()
-
- /**
- * Returns the value of field 'name'. The field 'name' has the
- * following description: Canonical name of application
- *
- * @return String
- * @return the value of field 'name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- } //-- java.lang.String getName()
-
- /**
- * Method getUser
- *
- *
- *
- * @param index
- * @return User
- */
- public org.vamsas.objects.core.User getUser(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _userList.size())) {
- throw new IndexOutOfBoundsException("getUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.User) _userList.elementAt(index);
- } //-- org.vamsas.objects.core.User getUser(int)
-
- /**
- * Method getUser
- *
- *
- *
- * @return User
- */
- public org.vamsas.objects.core.User[] getUser()
- {
- int size = _userList.size();
- org.vamsas.objects.core.User[] mArray = new org.vamsas.objects.core.User[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.User) _userList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.User[] getUser()
-
- /**
- * Method getUserCount
- *
- *
- *
- * @return int
- */
- public int getUserCount()
- {
- return _userList.size();
- } //-- int getUserCount()
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Version string describing the
- * application specific
- * data storage version used
- *
- * @return String
- * @return the value of field 'version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- } //-- java.lang.String 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)
-
- /**
- * Method removeAllInstance
- *
- */
- public void removeAllInstance()
- {
- _instanceList.removeAllElements();
- } //-- void removeAllInstance()
-
- /**
- * Method removeAllUser
- *
- */
- public void removeAllUser()
- {
- _userList.removeAllElements();
- } //-- void removeAllUser()
-
- /**
- * Method removeInstance
- *
- *
- *
- * @param index
- * @return Instance
- */
- public org.vamsas.objects.core.Instance removeInstance(int index)
- {
- java.lang.Object obj = _instanceList.elementAt(index);
- _instanceList.removeElementAt(index);
- return (org.vamsas.objects.core.Instance) obj;
- } //-- org.vamsas.objects.core.Instance removeInstance(int)
-
- /**
- * Method removeUser
- *
- *
- *
- * @param index
- * @return User
- */
- public org.vamsas.objects.core.User removeUser(int index)
- {
- java.lang.Object obj = _userList.elementAt(index);
- _userList.removeElementAt(index);
- return (org.vamsas.objects.core.User) obj;
- } //-- org.vamsas.objects.core.User removeUser(int)
-
- /**
- * Sets the value of field 'common'.
- *
- * @param common the value of field 'common'.
- */
- public void setCommon(org.vamsas.objects.core.Common common)
- {
- this._common = common;
- } //-- void setCommon(org.vamsas.objects.core.Common)
-
- /**
- * Method setInstance
- *
- *
- *
- * @param index
- * @param vInstance
- */
- public void setInstance(int index, org.vamsas.objects.core.Instance vInstance)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _instanceList.size())) {
- throw new IndexOutOfBoundsException("setInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]");
- }
- _instanceList.setElementAt(vInstance, index);
- } //-- void setInstance(int, org.vamsas.objects.core.Instance)
-
- /**
- * Method setInstance
- *
- *
- *
- * @param instanceArray
- */
- public void setInstance(org.vamsas.objects.core.Instance[] instanceArray)
- {
- //-- copy array
- _instanceList.removeAllElements();
- for (int i = 0; i < instanceArray.length; i++) {
- _instanceList.addElement(instanceArray[i]);
- }
- } //-- void setInstance(org.vamsas.objects.core.Instance)
-
- /**
- * Sets the value of field 'name'. The field 'name' has the
- * following description: Canonical name of application
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.String name)
- {
- this._name = name;
- } //-- void setName(java.lang.String)
-
- /**
- * Method setUser
- *
- *
- *
- * @param index
- * @param vUser
- */
- public void setUser(int index, org.vamsas.objects.core.User vUser)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _userList.size())) {
- throw new IndexOutOfBoundsException("setUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]");
- }
- _userList.setElementAt(vUser, index);
- } //-- void setUser(int, org.vamsas.objects.core.User)
-
- /**
- * Method setUser
- *
- *
- *
- * @param userArray
- */
- public void setUser(org.vamsas.objects.core.User[] userArray)
- {
- //-- copy array
- _userList.removeAllElements();
- for (int i = 0; i < userArray.length; i++) {
- _userList.addElement(userArray[i]);
- }
- } //-- void setUser(org.vamsas.objects.core.User)
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Version string describing the
- * application specific
- * data storage version used
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(java.lang.String version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return AppData
- */
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader);
- } //-- org.vamsas.objects.core.AppData 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class ApplicationDataDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ApplicationDataDescriptor extends org.vamsas.objects.core.AppDataDescriptor {
-
-
- //--------------------------/
- //- 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();
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());
- 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
-
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ApplicationData target = (ApplicationData) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.setVersion( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- 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.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ApplicationData target = (ApplicationData) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.setName( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _userList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ApplicationData target = (ApplicationData) object;
- return target.getUser();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.addUser( (org.vamsas.objects.core.User) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.User();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _userList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _common
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Common.class, "_common", "Common", 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.getCommon();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.setCommon( (org.vamsas.objects.core.Common) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Common();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _common
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _instanceList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Instance.class, "_instanceList", "Instance", 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.getInstance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.addInstance( (org.vamsas.objects.core.Instance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Instance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _instanceList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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 super.getExtends();
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- if (identity == null)
- return super.getIdentity();
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Attachment.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Attachment extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * true implies data will be decompresses with Zip\r
- * before presenting to application \r
- */\r
- private boolean _compressed = false;\r
-\r
- /**\r
- * keeps track of state for field: _compressed\r
- */\r
- private boolean _has_compressed;\r
-\r
- /**\r
- * Type of arbitrary data - TODO: decide format - use\r
- * (extended) MIME types ? \r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Object the arbitrary data is associated with\r
- * \r
- */\r
- private java.lang.Object _objectref;\r
-\r
- /**\r
- * Primary Key for vamsas object referencing\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Attachment() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Attachment()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteCompressed\r
- * \r
- */\r
- public void deleteCompressed()\r
- {\r
- this._has_compressed= false;\r
- } //-- void deleteCompressed() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Attachment) {\r
- \r
- Attachment temp = (Attachment)obj;\r
- if (this._compressed != temp._compressed)\r
- return false;\r
- if (this._has_compressed != temp._has_compressed)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- if (this._objectref != null) {\r
- if (temp._objectref == null) return false;\r
- else if (!(this._objectref.equals(temp._objectref))) \r
- return false;\r
- }\r
- else if (temp._objectref != null)\r
- return false;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
- }\r
- else if (temp._id != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'compressed'. The field\r
- * 'compressed' has the following description: true implies\r
- * data will be decompresses with Zip\r
- * before presenting to application \r
- * \r
- * @return boolean\r
- * @return the value of field 'compressed'.\r
- */\r
- public boolean getCompressed()\r
- {\r
- return this._compressed;\r
- } //-- boolean getCompressed() \r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'objectref'. The field\r
- * 'objectref' has the following description: Object the\r
- * arbitrary data is associated with\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'objectref'.\r
- */\r
- public java.lang.Object getObjectref()\r
- {\r
- return this._objectref;\r
- } //-- java.lang.Object getObjectref() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: Type of arbitrary data - TODO: decide\r
- * format - use\r
- * (extended) MIME types ? \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method hasCompressed\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasCompressed()\r
- {\r
- return this._has_compressed;\r
- } //-- boolean hasCompressed() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'compressed'. The field 'compressed'\r
- * has the following description: true implies data will be\r
- * decompresses with Zip\r
- * before presenting to application \r
- * \r
- * @param compressed the value of field 'compressed'.\r
- */\r
- public void setCompressed(boolean compressed)\r
- {\r
- this._compressed = compressed;\r
- this._has_compressed = true;\r
- } //-- void setCompressed(boolean) \r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'objectref'. The field 'objectref'\r
- * has the following description: Object the arbitrary data is\r
- * associated with\r
- * \r
- * \r
- * @param objectref the value of field 'objectref'.\r
- */\r
- public void setObjectref(java.lang.Object objectref)\r
- {\r
- this._objectref = objectref;\r
- } //-- void setObjectref(java.lang.Object) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: Type of arbitrary data - TODO: decide\r
- * format - use\r
- * (extended) MIME types ? \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(org.vamsas.objects.core.Attachment.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AttachmentDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AttachmentDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AttachmentDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Attachment";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _compressed\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_compressed", "compressed", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- if(!target.hasCompressed())\r
- return null;\r
- return (target.getCompressed() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteCompressed();\r
- return;\r
- }\r
- target.setCompressed( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _compressed\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _objectref\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objectref", "objectref", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getObjectref();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setObjectref( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _objectref\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
- this.identity = desc;\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getId();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setId( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.AttachmentDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Attachment.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Common.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Common extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Common() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Common()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Common) {\r
- \r
- Common temp = (Common)obj;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Common) Unmarshaller.unmarshal(org.vamsas.objects.core.Common.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class CommonDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class CommonDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public CommonDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Common";\r
- } //-- org.vamsas.objects.core.CommonDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Common.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:DataSet.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class DataSet.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class DataSet extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Field _sequenceList
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _dataSetAnnotationsList
- */
- private java.util.Vector _dataSetAnnotationsList;
-
- /**
- * Field _alignmentList
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DataSet()
- {
- super();
- _sequenceList = new Vector();
- _dataSetAnnotationsList = new Vector();
- _alignmentList = new Vector();
- _treeList = new Vector();
- } //-- org.vamsas.objects.core.DataSet()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param vAlignment
- */
- public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.addElement(vAlignment);
- } //-- void addAlignment(org.vamsas.objects.core.Alignment)
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.insertElementAt(vAlignment, index);
- } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
-
- /**
- * Method addDataSetAnnotations
- *
- *
- *
- * @param vDataSetAnnotations
- */
- public void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetAnnotationsList.addElement(vDataSetAnnotations);
- } //-- void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method addDataSetAnnotations
- *
- *
- *
- * @param index
- * @param vDataSetAnnotations
- */
- public void addDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index);
- } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param vSequence
- */
- public void addSequence(org.vamsas.objects.core.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.addElement(vSequence);
- } //-- void addSequence(org.vamsas.objects.core.Sequence)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.insertElementAt(vSequence, index);
- } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, org.vamsas.objects.core.Tree)
-
- /**
- * Method enumerateAlignment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return _alignmentList.elements();
- } //-- java.util.Enumeration enumerateAlignment()
-
- /**
- * Method enumerateDataSetAnnotations
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDataSetAnnotations()
- {
- return _dataSetAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateDataSetAnnotations()
-
- /**
- * Method enumerateSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequence()
- {
- return _sequenceList.elements();
- } //-- java.util.Enumeration enumerateSequence()
-
- /**
- * 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 DataSet) {
-
- DataSet temp = (DataSet)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._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._dataSetAnnotationsList != null) {
- if (temp._dataSetAnnotationsList == null) return false;
- else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)))
- return false;
- }
- else if (temp._dataSetAnnotationsList != 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._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._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 getAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.objects.core.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.objects.core.Alignment) _alignmentList.elementAt(index);
- } //-- org.vamsas.objects.core.Alignment getAlignment(int)
-
- /**
- * Method getAlignment
- *
- *
- *
- * @return Alignment
- */
- public org.vamsas.objects.core.Alignment[] getAlignment()
- {
- int size = _alignmentList.size();
- org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Alignment[] getAlignment()
-
- /**
- * Method getAlignmentCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentCount()
- {
- return _alignmentList.size();
- } //-- int getAlignmentCount()
-
- /**
- * Method getDataSetAnnotations
- *
- *
- *
- * @param index
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
- } //-- org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int)
-
- /**
- * Method getDataSetAnnotations
- *
- *
- *
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
- {
- int size = _dataSetAnnotationsList.size();
- org.vamsas.objects.core.DataSetAnnotations[] mArray = new org.vamsas.objects.core.DataSetAnnotations[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
-
- /**
- * Method getDataSetAnnotationsCount
- *
- *
- *
- * @return int
- */
- public int getDataSetAnnotationsCount()
- {
- return _dataSetAnnotationsList.size();
- } //-- int getDataSetAnnotationsCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Method getSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.objects.core.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.objects.core.Sequence) _sequenceList.elementAt(index);
- } //-- org.vamsas.objects.core.Sequence getSequence(int)
-
- /**
- * Method getSequence
- *
- *
- *
- * @return Sequence
- */
- public org.vamsas.objects.core.Sequence[] getSequence()
- {
- int size = _sequenceList.size();
- org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Sequence[] getSequence()
-
- /**
- * Method getSequenceCount
- *
- *
- *
- * @return int
- */
- public int getSequenceCount()
- {
- return _sequenceList.size();
- } //-- int getSequenceCount()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index);
- } //-- org.vamsas.objects.core.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public org.vamsas.objects.core.Tree[] getTree()
- {
- int size = _treeList.size();
- org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Tree[] getTree()
-
- /**
- * 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 removeAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.objects.core.Alignment removeAlignment(int index)
- {
- java.lang.Object obj = _alignmentList.elementAt(index);
- _alignmentList.removeElementAt(index);
- return (org.vamsas.objects.core.Alignment) obj;
- } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
-
- /**
- * Method removeAllAlignment
- *
- */
- public void removeAllAlignment()
- {
- _alignmentList.removeAllElements();
- } //-- void removeAllAlignment()
-
- /**
- * Method removeAllDataSetAnnotations
- *
- */
- public void removeAllDataSetAnnotations()
- {
- _dataSetAnnotationsList.removeAllElements();
- } //-- void removeAllDataSetAnnotations()
-
- /**
- * Method removeAllSequence
- *
- */
- public void removeAllSequence()
- {
- _sequenceList.removeAllElements();
- } //-- void removeAllSequence()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeDataSetAnnotations
- *
- *
- *
- * @param index
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
- {
- java.lang.Object obj = _dataSetAnnotationsList.elementAt(index);
- _dataSetAnnotationsList.removeElementAt(index);
- return (org.vamsas.objects.core.DataSetAnnotations) obj;
- } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int)
-
- /**
- * Method removeSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.objects.core.Sequence removeSequence(int index)
- {
- java.lang.Object obj = _sequenceList.elementAt(index);
- _sequenceList.removeElementAt(index);
- return (org.vamsas.objects.core.Sequence) obj;
- } //-- org.vamsas.objects.core.Sequence removeSequence(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (org.vamsas.objects.core.Tree) obj;
- } //-- org.vamsas.objects.core.Tree removeTree(int)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void setAlignment(int index, org.vamsas.objects.core.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.objects.core.Alignment)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param alignmentArray
- */
- public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
- {
- //-- copy array
- _alignmentList.removeAllElements();
- for (int i = 0; i < alignmentArray.length; i++) {
- _alignmentList.addElement(alignmentArray[i]);
- }
- } //-- void setAlignment(org.vamsas.objects.core.Alignment)
-
- /**
- * Method setDataSetAnnotations
- *
- *
- *
- * @param index
- * @param vDataSetAnnotations
- */
- public void setDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
- }
- _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index);
- } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method setDataSetAnnotations
- *
- *
- *
- * @param dataSetAnnotationsArray
- */
- public void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray)
- {
- //-- copy array
- _dataSetAnnotationsList.removeAllElements();
- for (int i = 0; i < dataSetAnnotationsArray.length; i++) {
- _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]);
- }
- } //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void setSequence(int index, org.vamsas.objects.core.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.objects.core.Sequence)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param sequenceArray
- */
- public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
- {
- //-- copy array
- _sequenceList.removeAllElements();
- for (int i = 0; i < sequenceArray.length; i++) {
- _sequenceList.addElement(sequenceArray[i]);
- }
- } //-- void setSequence(org.vamsas.objects.core.Sequence)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(org.vamsas.objects.core.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return DataSet
- */
- public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader);
- } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class DataSetAnnotations.
- *
- * @version $Revision$ $Date$
- */
-public class DataSetAnnotations extends org.vamsas.objects.core.RangeAnnotation
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * annotation is associated with a
- * particular dataset sequence
- */
- private java.lang.Object _seqRef;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DataSetAnnotations()
- {
- super();
- } //-- org.vamsas.objects.core.DataSetAnnotations()
-
-
- //-----------/
- //- 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 DataSetAnnotations) {
-
- DataSetAnnotations temp = (DataSetAnnotations)obj;
- 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._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 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Returns the value of field 'seqRef'. The field 'seqRef' has
- * the following description: annotation is associated with a
- * particular dataset sequence
- *
- * @return Object
- * @return the value of field 'seqRef'.
- */
- public java.lang.Object getSeqRef()
- {
- return this._seqRef;
- } //-- java.lang.Object getSeqRef()
-
- /**
- * 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 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Sets the value of field 'seqRef'. The field 'seqRef' has the
- * following description: annotation is associated with a
- * particular dataset sequence
- *
- * @param seqRef the value of field 'seqRef'.
- */
- public void setSeqRef(java.lang.Object seqRef)
- {
- this._seqRef = seqRef;
- } //-- void setSeqRef(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return RangeType
- */
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader);
- } //-- org.vamsas.objects.core.RangeType 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class DataSetAnnotationsDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class DataSetAnnotationsDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {
-
-
- //--------------------------/
- //- 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 DataSetAnnotationsDescriptor()
- {
- super();
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "DataSetAnnotations";
-
- //-- 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
-
- //-- _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
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getSeqRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) 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
-
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.DataSetAnnotationsDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return super.getExtends();
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- if (identity == null)
- return super.getIdentity();
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.DataSetAnnotations.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class DataSetDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class DataSetDescriptor 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 DataSetDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "DataSet";
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSet target = (DataSet) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _sequenceList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSet target = (DataSet) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.addSequence( (org.vamsas.objects.core.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.objects.core.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);
- //-- _dataSetAnnotationsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSet target = (DataSet) object;
- return target.getDataSetAnnotations();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.addDataSetAnnotations( (org.vamsas.objects.core.DataSetAnnotations) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.DataSetAnnotations();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dataSetAnnotationsList
- 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.objects.core.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
- {
- DataSet target = (DataSet) object;
- return target.getAlignment();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.addAlignment( (org.vamsas.objects.core.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.objects.core.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);
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSet target = (DataSet) object;
- return target.getTree();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.addTree( (org.vamsas.objects.core.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.objects.core.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);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSet target = (DataSet) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSet target = (DataSet) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.DataSetDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return null;
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.DataSet.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:DbRef.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Store a list of database references
- * for this sequence record - with optional mapping
- * from database sequence to the given sequence record
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class DbRef extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- */
- private java.lang.String _source;
-
- /**
- * Version must be specified -
- *
- */
- private java.lang.String _version;
-
- /**
- * TODO: make some specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- */
- private java.lang.String _accessionId;
-
- /**
- * Primary Key for vamsas object
- * referencing
- */
- private java.lang.String _id;
-
- /**
- * From: Offset to first
- * position in dataset sequence record that
- * this database entry maps to To: Offset
- * to last position in dataset sequence
- * record that this database entry maps to
- * Start: Offset to first last position in
- * database entry that first (or offset)
- * position in sequence maps to End: Offset
- * to last position in database entry that
- * last (offset) position in sequence maps
- * to
- */
- private java.util.Vector _mapList;
-
- /**
- * Field _linkList
- */
- private java.util.Vector _linkList;
-
- /**
- * Field _propertyList
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DbRef()
- {
- super();
- _mapList = new Vector();
- _linkList = new Vector();
- _propertyList = new Vector();
- } //-- org.vamsas.objects.core.DbRef()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addLink
- *
- *
- *
- * @param vLink
- */
- public void addLink(org.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- _linkList.addElement(vLink);
- } //-- void addLink(org.vamsas.objects.core.Link)
-
- /**
- * Method addLink
- *
- *
- *
- * @param index
- * @param vLink
- */
- public void addLink(int index, org.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- _linkList.insertElementAt(vLink, index);
- } //-- void addLink(int, org.vamsas.objects.core.Link)
-
- /**
- * Method addMap
- *
- *
- *
- * @param vMap
- */
- public void addMap(org.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- _mapList.addElement(vMap);
- } //-- void addMap(org.vamsas.objects.core.Map)
-
- /**
- * Method addMap
- *
- *
- *
- * @param index
- * @param vMap
- */
- public void addMap(int index, org.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- _mapList.insertElementAt(vMap, index);
- } //-- void addMap(int, org.vamsas.objects.core.Map)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method enumerateLink
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateLink()
- {
- return _linkList.elements();
- } //-- java.util.Enumeration enumerateLink()
-
- /**
- * Method enumerateMap
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateMap()
- {
- return _mapList.elements();
- } //-- java.util.Enumeration enumerateMap()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._mapList != null) {
- if (temp._mapList == null) return false;
- else if (!(this._mapList.equals(temp._mapList)))
- return false;
- }
- else if (temp._mapList != null)
- return false;
- if (this._linkList != null) {
- if (temp._linkList == null) return false;
- else if (!(this._linkList.equals(temp._linkList)))
- return false;
- }
- else if (temp._linkList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'accessionId'. The field
- * 'accessionId' has the following description: TODO: make some
- * specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- *
- * @return String
- * @return the value of field 'accessionId'.
- */
- public java.lang.String getAccessionId()
- {
- return this._accessionId;
- } //-- java.lang.String getAccessionId()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getLink
- *
- *
- *
- * @param index
- * @return Link
- */
- public org.vamsas.objects.core.Link getLink(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _linkList.size())) {
- throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Link) _linkList.elementAt(index);
- } //-- org.vamsas.objects.core.Link getLink(int)
-
- /**
- * Method getLink
- *
- *
- *
- * @return Link
- */
- public org.vamsas.objects.core.Link[] getLink()
- {
- int size = _linkList.size();
- org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Link[] getLink()
-
- /**
- * Method getLinkCount
- *
- *
- *
- * @return int
- */
- public int getLinkCount()
- {
- return _linkList.size();
- } //-- int getLinkCount()
-
- /**
- * Method getMap
- *
- *
- *
- * @param index
- * @return Map
- */
- public org.vamsas.objects.core.Map getMap(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mapList.size())) {
- throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Map) _mapList.elementAt(index);
- } //-- org.vamsas.objects.core.Map getMap(int)
-
- /**
- * Method getMap
- *
- *
- *
- * @return Map
- */
- public org.vamsas.objects.core.Map[] getMap()
- {
- int size = _mapList.size();
- org.vamsas.objects.core.Map[] mArray = new org.vamsas.objects.core.Map[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Map) _mapList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Map[] getMap()
-
- /**
- * Method getMapCount
- *
- *
- *
- * @return int
- */
- public int getMapCount()
- {
- return _mapList.size();
- } //-- int getMapCount()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'source'. The field 'source' has
- * the following description: TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- *
- * @return String
- * @return the value of field 'source'.
- */
- public java.lang.String getSource()
- {
- return this._source;
- } //-- java.lang.String getSource()
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Version must be specified -
- *
- *
- * @return String
- * @return the value of field 'version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- } //-- java.lang.String 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)
-
- /**
- * Method removeAllLink
- *
- */
- public void removeAllLink()
- {
- _linkList.removeAllElements();
- } //-- void removeAllLink()
-
- /**
- * Method removeAllMap
- *
- */
- public void removeAllMap()
- {
- _mapList.removeAllElements();
- } //-- void removeAllMap()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeLink
- *
- *
- *
- * @param index
- * @return Link
- */
- public org.vamsas.objects.core.Link removeLink(int index)
- {
- java.lang.Object obj = _linkList.elementAt(index);
- _linkList.removeElementAt(index);
- return (org.vamsas.objects.core.Link) obj;
- } //-- org.vamsas.objects.core.Link removeLink(int)
-
- /**
- * Method removeMap
- *
- *
- *
- * @param index
- * @return Map
- */
- public org.vamsas.objects.core.Map removeMap(int index)
- {
- java.lang.Object obj = _mapList.elementAt(index);
- _mapList.removeElementAt(index);
- return (org.vamsas.objects.core.Map) obj;
- } //-- org.vamsas.objects.core.Map removeMap(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Sets the value of field 'accessionId'. The field
- * 'accessionId' has the following description: TODO: make some
- * specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- *
- * @param accessionId the value of field 'accessionId'.
- */
- public void setAccessionId(java.lang.String accessionId)
- {
- this._accessionId = accessionId;
- } //-- void setAccessionId(java.lang.String)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setLink
- *
- *
- *
- * @param index
- * @param vLink
- */
- public void setLink(int index, org.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _linkList.size())) {
- throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
- }
- _linkList.setElementAt(vLink, index);
- } //-- void setLink(int, org.vamsas.objects.core.Link)
-
- /**
- * Method setLink
- *
- *
- *
- * @param linkArray
- */
- public void setLink(org.vamsas.objects.core.Link[] linkArray)
- {
- //-- copy array
- _linkList.removeAllElements();
- for (int i = 0; i < linkArray.length; i++) {
- _linkList.addElement(linkArray[i]);
- }
- } //-- void setLink(org.vamsas.objects.core.Link)
-
- /**
- * Method setMap
- *
- *
- *
- * @param index
- * @param vMap
- */
- public void setMap(int index, org.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mapList.size())) {
- throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
- }
- _mapList.setElementAt(vMap, index);
- } //-- void setMap(int, org.vamsas.objects.core.Map)
-
- /**
- * Method setMap
- *
- *
- *
- * @param mapArray
- */
- public void setMap(org.vamsas.objects.core.Map[] mapArray)
- {
- //-- copy array
- _mapList.removeAllElements();
- for (int i = 0; i < mapArray.length; i++) {
- _mapList.addElement(mapArray[i]);
- }
- } //-- void setMap(org.vamsas.objects.core.Map)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * Sets the value of field 'source'. The field 'source' has the
- * following description: TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- *
- * @param source the value of field 'source'.
- */
- public void setSource(java.lang.String source)
- {
- this._source = source;
- } //-- void setSource(java.lang.String)
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Version must be specified -
- *
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(java.lang.String version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return DbRef
- */
- public static org.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader);
- } //-- org.vamsas.objects.core.DbRef unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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";
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _source
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getSource();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setSource( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _source
- 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);
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setVersion( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- 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);
- //-- _accessionId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getAccessionId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setAccessionId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _accessionId
- 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);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _mapList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Map.class, "_mapList", "map", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getMap();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.addMap( (org.vamsas.objects.core.Map) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Map();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mapList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _linkList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getLink();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.addLink( (org.vamsas.objects.core.Link) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Link();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _linkList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.addProperty( (org.vamsas.objects.core.Property) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Entry.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Entry.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class Entry extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * Who
- */
- private java.lang.String _user;
-
- /**
- * With which application
- */
- private java.lang.String _app;
-
- /**
- * Did what
- */
- private java.lang.String _action;
-
- /**
- * When
- */
- private org.exolab.castor.types.Date _date;
-
- /**
- * additional information
- */
- private java.util.Vector _propertyList;
-
- /**
- * parameter for the action
- */
- private java.util.Vector _paramList;
-
- /**
- * bioinformatic objects input to action
- *
- */
- private java.util.Vector _inputList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Entry()
- {
- super();
- _propertyList = new Vector();
- _paramList = new Vector();
- _inputList = new Vector();
- } //-- org.vamsas.objects.core.Entry()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addInput
- *
- *
- *
- * @param vInput
- */
- public void addInput(org.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- _inputList.addElement(vInput);
- } //-- void addInput(org.vamsas.objects.core.Input)
-
- /**
- * Method addInput
- *
- *
- *
- * @param index
- * @param vInput
- */
- public void addInput(int index, org.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- _inputList.insertElementAt(vInput, index);
- } //-- void addInput(int, org.vamsas.objects.core.Input)
-
- /**
- * Method addParam
- *
- *
- *
- * @param vParam
- */
- public void addParam(org.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- _paramList.addElement(vParam);
- } //-- void addParam(org.vamsas.objects.core.Param)
-
- /**
- * Method addParam
- *
- *
- *
- * @param index
- * @param vParam
- */
- public void addParam(int index, org.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- _paramList.insertElementAt(vParam, index);
- } //-- void addParam(int, org.vamsas.objects.core.Param)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method enumerateInput
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateInput()
- {
- return _inputList.elements();
- } //-- java.util.Enumeration enumerateInput()
-
- /**
- * Method enumerateParam
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateParam()
- {
- return _paramList.elements();
- } //-- java.util.Enumeration enumerateParam()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._user != null) {
- if (temp._user == null) return false;
- else if (!(this._user.equals(temp._user)))
- return false;
- }
- else if (temp._user != null)
- return false;
- if (this._app != null) {
- if (temp._app == null) return false;
- else if (!(this._app.equals(temp._app)))
- return false;
- }
- else if (temp._app != 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;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != null)
- return false;
- if (this._paramList != null) {
- if (temp._paramList == null) return false;
- else if (!(this._paramList.equals(temp._paramList)))
- return false;
- }
- else if (temp._paramList != null)
- return false;
- if (this._inputList != null) {
- if (temp._inputList == null) return false;
- else if (!(this._inputList.equals(temp._inputList)))
- return false;
- }
- else if (temp._inputList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'action'. The field 'action' has
- * the following description: Did what
- *
- * @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 'app'. The field 'app' has the
- * following description: With which application
- *
- * @return String
- * @return the value of field 'app'.
- */
- public java.lang.String getApp()
- {
- return this._app;
- } //-- java.lang.String getApp()
-
- /**
- * Returns the value of field 'date'. The field 'date' has the
- * following description: When
- *
- * @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 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getInput
- *
- *
- *
- * @param index
- * @return Input
- */
- public org.vamsas.objects.core.Input getInput(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _inputList.size())) {
- throw new IndexOutOfBoundsException("getInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Input) _inputList.elementAt(index);
- } //-- org.vamsas.objects.core.Input getInput(int)
-
- /**
- * Method getInput
- *
- *
- *
- * @return Input
- */
- public org.vamsas.objects.core.Input[] getInput()
- {
- int size = _inputList.size();
- org.vamsas.objects.core.Input[] mArray = new org.vamsas.objects.core.Input[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Input) _inputList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Input[] getInput()
-
- /**
- * Method getInputCount
- *
- *
- *
- * @return int
- */
- public int getInputCount()
- {
- return _inputList.size();
- } //-- int getInputCount()
-
- /**
- * Method getParam
- *
- *
- *
- * @param index
- * @return Param
- */
- public org.vamsas.objects.core.Param getParam(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _paramList.size())) {
- throw new IndexOutOfBoundsException("getParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Param) _paramList.elementAt(index);
- } //-- org.vamsas.objects.core.Param getParam(int)
-
- /**
- * Method getParam
- *
- *
- *
- * @return Param
- */
- public org.vamsas.objects.core.Param[] getParam()
- {
- int size = _paramList.size();
- org.vamsas.objects.core.Param[] mArray = new org.vamsas.objects.core.Param[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Param) _paramList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Param[] getParam()
-
- /**
- * Method getParamCount
- *
- *
- *
- * @return int
- */
- public int getParamCount()
- {
- return _paramList.size();
- } //-- int getParamCount()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'user'. The field 'user' has the
- * following description: Who
- *
- * @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)
-
- /**
- * Method removeAllInput
- *
- */
- public void removeAllInput()
- {
- _inputList.removeAllElements();
- } //-- void removeAllInput()
-
- /**
- * Method removeAllParam
- *
- */
- public void removeAllParam()
- {
- _paramList.removeAllElements();
- } //-- void removeAllParam()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeInput
- *
- *
- *
- * @param index
- * @return Input
- */
- public org.vamsas.objects.core.Input removeInput(int index)
- {
- java.lang.Object obj = _inputList.elementAt(index);
- _inputList.removeElementAt(index);
- return (org.vamsas.objects.core.Input) obj;
- } //-- org.vamsas.objects.core.Input removeInput(int)
-
- /**
- * Method removeParam
- *
- *
- *
- * @param index
- * @return Param
- */
- public org.vamsas.objects.core.Param removeParam(int index)
- {
- java.lang.Object obj = _paramList.elementAt(index);
- _paramList.removeElementAt(index);
- return (org.vamsas.objects.core.Param) obj;
- } //-- org.vamsas.objects.core.Param removeParam(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Sets the value of field 'action'. The field 'action' has the
- * following description: Did what
- *
- * @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 'app'. The field 'app' has the
- * following description: With which application
- *
- * @param app the value of field 'app'.
- */
- public void setApp(java.lang.String app)
- {
- this._app = app;
- } //-- void setApp(java.lang.String)
-
- /**
- * Sets the value of field 'date'. The field 'date' has the
- * following description: When
- *
- * @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 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setInput
- *
- *
- *
- * @param index
- * @param vInput
- */
- public void setInput(int index, org.vamsas.objects.core.Input vInput)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _inputList.size())) {
- throw new IndexOutOfBoundsException("setInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
- }
- _inputList.setElementAt(vInput, index);
- } //-- void setInput(int, org.vamsas.objects.core.Input)
-
- /**
- * Method setInput
- *
- *
- *
- * @param inputArray
- */
- public void setInput(org.vamsas.objects.core.Input[] inputArray)
- {
- //-- copy array
- _inputList.removeAllElements();
- for (int i = 0; i < inputArray.length; i++) {
- _inputList.addElement(inputArray[i]);
- }
- } //-- void setInput(org.vamsas.objects.core.Input)
-
- /**
- * Method setParam
- *
- *
- *
- * @param index
- * @param vParam
- */
- public void setParam(int index, org.vamsas.objects.core.Param vParam)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _paramList.size())) {
- throw new IndexOutOfBoundsException("setParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
- }
- _paramList.setElementAt(vParam, index);
- } //-- void setParam(int, org.vamsas.objects.core.Param)
-
- /**
- * Method setParam
- *
- *
- *
- * @param paramArray
- */
- public void setParam(org.vamsas.objects.core.Param[] paramArray)
- {
- //-- copy array
- _paramList.removeAllElements();
- for (int i = 0; i < paramArray.length; i++) {
- _paramList.addElement(paramArray[i]);
- }
- } //-- void setParam(org.vamsas.objects.core.Param)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * Sets the value of field 'user'. The field 'user' has the
- * following description: Who
- *
- * @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.objects.core.Entry unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader);
- } //-- org.vamsas.objects.core.Entry unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Entry target = (Entry) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _user
- 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);
- //-- _app
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_app", "App", 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.getApp();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.setApp( (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: _app
- 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);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Entry target = (Entry) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.addProperty( (org.vamsas.objects.core.Property) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _paramList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Param.class, "_paramList", "param", 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.getParam();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.addParam( (org.vamsas.objects.core.Param) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Param();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _paramList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _inputList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Input.class, "_inputList", "input", 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.getInput();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.addInput( (org.vamsas.objects.core.Input) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Input();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _inputList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Discrete symbol - possibly graphically represented\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Glyph extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * specifies the symbol dictionary for this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- */\r
- private java.lang.String _dict = "utf8";\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Glyph() \r
- {\r
- super();\r
- setContent("");\r
- setDict("utf8");\r
- } //-- org.vamsas.objects.core.Glyph()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Glyph) {\r
- \r
- Glyph temp = (Glyph)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._dict != null) {\r
- if (temp._dict == null) return false;\r
- else if (!(this._dict.equals(temp._dict))) \r
- return false;\r
- }\r
- else if (temp._dict != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'dict'. The field 'dict' has the\r
- * following description: specifies the symbol dictionary for\r
- * this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- * \r
- * @return String\r
- * @return the value of field 'dict'.\r
- */\r
- public java.lang.String getDict()\r
- {\r
- return this._dict;\r
- } //-- java.lang.String getDict() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'dict'. The field 'dict' has the\r
- * following description: specifies the symbol dictionary for\r
- * this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- * \r
- * @param dict the value of field 'dict'.\r
- */\r
- public void setDict(java.lang.String dict)\r
- {\r
- this._dict = dict;\r
- } //-- void setDict(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Glyph\r
- */\r
- public static org.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(org.vamsas.objects.core.Glyph.class, reader);\r
- } //-- org.vamsas.objects.core.Glyph unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class GlyphDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class GlyphDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public GlyphDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "glyph";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Glyph target = (Glyph) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Glyph target = (Glyph) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _dict\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dict", "dict", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Glyph target = (Glyph) object;\r
- return target.getDict();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Glyph target = (Glyph) object;\r
- target.setDict( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _dict\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.GlyphDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Glyph.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Input.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Input extends org.vamsas.objects.core.RangeType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Reference Frame for rangeType specfication\r
- * \r
- */\r
- private java.lang.Object _objRef;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Input() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Input()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Input) {\r
- \r
- Input temp = (Input)obj;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._objRef != null) {\r
- if (temp._objRef == null) return false;\r
- else if (!(this._objRef.equals(temp._objRef))) \r
- return false;\r
- }\r
- else if (temp._objRef != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'objRef'. The field 'objRef' has\r
- * the following description: Reference Frame for rangeType\r
- * specfication\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'objRef'.\r
- */\r
- public java.lang.Object getObjRef()\r
- {\r
- return this._objRef;\r
- } //-- java.lang.Object getObjRef() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'objRef'. The field 'objRef' has the\r
- * following description: Reference Frame for rangeType\r
- * specfication\r
- * \r
- * \r
- * @param objRef the value of field 'objRef'.\r
- */\r
- public void setObjRef(java.lang.Object objRef)\r
- {\r
- this._objRef = objRef;\r
- } //-- void setObjRef(java.lang.Object) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Input) Unmarshaller.unmarshal(org.vamsas.objects.core.Input.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class InputDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class InputDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public InputDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "input";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Input target = (Input) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Input target = (Input) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _objRef\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objRef", "objRef", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Input target = (Input) object;\r
- return target.getObjRef();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Input target = (Input) object;\r
- target.setObjRef( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _objRef\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.InputDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Input.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Instance.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Instance extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _urn\r
- */\r
- private java.lang.String _urn;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Instance() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Instance()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Instance) {\r
- \r
- Instance temp = (Instance)obj;\r
- if (this._urn != null) {\r
- if (temp._urn == null) return false;\r
- else if (!(this._urn.equals(temp._urn))) \r
- return false;\r
- }\r
- else if (temp._urn != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'urn'.\r
- * \r
- * @return String\r
- * @return the value of field 'urn'.\r
- */\r
- public java.lang.String getUrn()\r
- {\r
- return this._urn;\r
- } //-- java.lang.String getUrn() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'urn'.\r
- * \r
- * @param urn the value of field 'urn'.\r
- */\r
- public void setUrn(java.lang.String urn)\r
- {\r
- this._urn = urn;\r
- } //-- void setUrn(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Instance) Unmarshaller.unmarshal(org.vamsas.objects.core.Instance.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class InstanceDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class InstanceDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public InstanceDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Instance";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _urn\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Instance target = (Instance) object;\r
- return target.getUrn();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Instance target = (Instance) object;\r
- target.setUrn( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _urn\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.InstanceDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Instance.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Link.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Link extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * The URI\r
- */\r
- private java.lang.String _href;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Link() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Link()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Link) {\r
- \r
- Link temp = (Link)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._href != null) {\r
- if (temp._href == null) return false;\r
- else if (!(this._href.equals(temp._href))) \r
- return false;\r
- }\r
- else if (temp._href != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'href'. The field 'href' has the\r
- * following description: The URI\r
- * \r
- * @return String\r
- * @return the value of field 'href'.\r
- */\r
- public java.lang.String getHref()\r
- {\r
- return this._href;\r
- } //-- java.lang.String getHref() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'href'. The field 'href' has the\r
- * following description: The URI\r
- * \r
- * @param href the value of field 'href'.\r
- */\r
- public void setHref(java.lang.String href)\r
- {\r
- this._href = href;\r
- } //-- void setHref(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Link\r
- */\r
- public static org.vamsas.objects.core.Link unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Link) Unmarshaller.unmarshal(org.vamsas.objects.core.Link.class, reader);\r
- } //-- org.vamsas.objects.core.Link unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class LinkDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class LinkDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public LinkDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "link";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Link target = (Link) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Link target = (Link) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _href\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_href", "href", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Link target = (Link) object;\r
- return target.getHref();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Link target = (Link) object;\r
- target.setHref( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _href\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.LinkDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Link.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:LockFile.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class LockFile.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class LockFile extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public LockFile()
- {
- super();
- setContent("");
- } //-- org.vamsas.objects.core.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.objects.core.LockFile unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.LockFile) Unmarshaller.unmarshal(org.vamsas.objects.core.LockFile.class, reader);
- } //-- org.vamsas.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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.ac.uk/vamsasDocument";
- 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.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * From: Offset to first\r
- * position in dataset sequence record that\r
- * this database entry maps to To: Offset\r
- * to last position in dataset sequence\r
- * record that this database entry maps to\r
- * Start: Offset to first last position in\r
- * database entry that first (or offset)\r
- * position in sequence maps to End: Offset\r
- * to last position in database entry that\r
- * last (offset) position in sequence maps\r
- * to \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Map extends org.vamsas.objects.core.MapList \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Map() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Map()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Map) {\r
- \r
- Map temp = (Map)obj;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Map) Unmarshaller.unmarshal(org.vamsas.objects.core.Map.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MapDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapDescriptor extends org.vamsas.objects.core.MapListDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "map";\r
- } //-- org.vamsas.objects.core.MapDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Map.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class MapList.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapList extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Offset to first position in dataset sequence record that\r
- * start\r
- * position on 'onto' maps to \r
- */\r
- private int _from = 0;\r
-\r
- /**\r
- * keeps track of state for field: _from\r
- */\r
- private boolean _has_from;\r
-\r
- /**\r
- * Offset to last position in dataset sequence record that end\r
- * position on 'onto' maps to \r
- */\r
- private int _to = 0;\r
-\r
- /**\r
- * keeps track of state for field: _to\r
- */\r
- private boolean _has_to;\r
-\r
- /**\r
- * Offset to first position in database entry that first (or\r
- * offset)\r
- * position in sequence maps to \r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Offset to last position in database entry that last (offset)\r
- * position in sequence maps to \r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapList() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.MapList()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteFrom\r
- * \r
- */\r
- public void deleteFrom()\r
- {\r
- this._has_from= false;\r
- } //-- void deleteFrom() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Method deleteTo\r
- * \r
- */\r
- public void deleteTo()\r
- {\r
- this._has_to= false;\r
- } //-- void deleteTo() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof MapList) {\r
- \r
- MapList temp = (MapList)obj;\r
- if (this._from != temp._from)\r
- return false;\r
- if (this._has_from != temp._has_from)\r
- return false;\r
- if (this._to != temp._to)\r
- return false;\r
- if (this._has_to != temp._has_to)\r
- return false;\r
- if (this._start != temp._start)\r
- return false;\r
- if (this._has_start != temp._has_start)\r
- return false;\r
- if (this._end != temp._end)\r
- return false;\r
- if (this._has_end != temp._has_end)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'end'. The field 'end' has the\r
- * following description: Offset to last position in database\r
- * entry that last (offset)\r
- * position in sequence maps to \r
- * \r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd() \r
-\r
- /**\r
- * Returns the value of field 'from'. The field 'from' has the\r
- * following description: Offset to first position in dataset\r
- * sequence record that start\r
- * position on 'onto' maps to \r
- * \r
- * @return int\r
- * @return the value of field 'from'.\r
- */\r
- public int getFrom()\r
- {\r
- return this._from;\r
- } //-- int getFrom() \r
-\r
- /**\r
- * Returns the value of field 'start'. The field 'start' has\r
- * the following description: Offset to first position in\r
- * database entry that first (or offset)\r
- * position in sequence maps to \r
- * \r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart() \r
-\r
- /**\r
- * Returns the value of field 'to'. The field 'to' has the\r
- * following description: Offset to last position in dataset\r
- * sequence record that end\r
- * position on 'onto' maps to \r
- * \r
- * @return int\r
- * @return the value of field 'to'.\r
- */\r
- public int getTo()\r
- {\r
- return this._to;\r
- } //-- int getTo() \r
-\r
- /**\r
- * Method hasEnd\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd() \r
-\r
- /**\r
- * Method hasFrom\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFrom()\r
- {\r
- return this._has_from;\r
- } //-- boolean hasFrom() \r
-\r
- /**\r
- * Method hasStart\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart() \r
-\r
- /**\r
- * Method hasTo\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasTo()\r
- {\r
- return this._has_to;\r
- } //-- boolean hasTo() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'end'. The field 'end' has the\r
- * following description: Offset to last position in database\r
- * entry that last (offset)\r
- * position in sequence maps to \r
- * \r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int) \r
-\r
- /**\r
- * Sets the value of field 'from'. The field 'from' has the\r
- * following description: Offset to first position in dataset\r
- * sequence record that start\r
- * position on 'onto' maps to \r
- * \r
- * @param from the value of field 'from'.\r
- */\r
- public void setFrom(int from)\r
- {\r
- this._from = from;\r
- this._has_from = true;\r
- } //-- void setFrom(int) \r
-\r
- /**\r
- * Sets the value of field 'start'. The field 'start' has the\r
- * following description: Offset to first position in database\r
- * entry that first (or offset)\r
- * position in sequence maps to \r
- * \r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int) \r
-\r
- /**\r
- * Sets the value of field 'to'. The field 'to' has the\r
- * following description: Offset to last position in dataset\r
- * sequence record that end\r
- * position on 'onto' maps to \r
- * \r
- * @param to the value of field 'to'.\r
- */\r
- public void setTo(int to)\r
- {\r
- this._to = to;\r
- this._has_to = true;\r
- } //-- void setTo(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.MapList) Unmarshaller.unmarshal(org.vamsas.objects.core.MapList.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MapListDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapListDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapListDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "mapList";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _from\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_from", "from", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasFrom())\r
- return null;\r
- return new java.lang.Integer(target.getFrom());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteFrom();\r
- return;\r
- }\r
- target.setFrom( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _from\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _to\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_to", "to", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasTo())\r
- return null;\r
- return new java.lang.Integer(target.getTo());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteTo();\r
- return;\r
- }\r
- target.setTo( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _to\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasStart())\r
- return null;\r
- return new java.lang.Integer(target.getStart());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setStart( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasEnd())\r
- return null;\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setEnd( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.MapListDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.MapList.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Mapping.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Mapping extends org.vamsas.objects.core.MapList \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * object to which the mapping is being mapped\r
- * \r
- */\r
- private java.lang.Object _onto;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Mapping() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Mapping()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Mapping) {\r
- \r
- Mapping temp = (Mapping)obj;\r
- if (this._onto != null) {\r
- if (temp._onto == null) return false;\r
- else if (!(this._onto.equals(temp._onto))) \r
- return false;\r
- }\r
- else if (temp._onto != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'onto'. The field 'onto' has the\r
- * following description: object to which the mapping is being\r
- * mapped\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'onto'.\r
- */\r
- public java.lang.Object getOnto()\r
- {\r
- return this._onto;\r
- } //-- java.lang.Object getOnto() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'onto'. The field 'onto' has the\r
- * following description: object to which the mapping is being\r
- * mapped\r
- * \r
- * \r
- * @param onto the value of field 'onto'.\r
- */\r
- public void setOnto(java.lang.Object onto)\r
- {\r
- this._onto = onto;\r
- } //-- void setOnto(java.lang.Object) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Mapping) Unmarshaller.unmarshal(org.vamsas.objects.core.Mapping.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MappingDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MappingDescriptor extends org.vamsas.objects.core.MapListDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MappingDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "mapping";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _onto\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_onto", "onto", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Mapping target = (Mapping) object;\r
- return target.getOnto();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Mapping target = (Mapping) object;\r
- target.setOnto( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _onto\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.MappingDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Mapping.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Newick.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Newick.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class Newick extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
- /**
- * Field _title
- */
- private java.lang.String _title;
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable
- */
- private java.lang.String _modifiable;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Newick()
- {
- super();
- setContent("");
- } //-- org.vamsas.objects.core.Newick()
-
-
- //-----------/
- //- 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 Newick) {
-
- Newick temp = (Newick)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;
- if (this._title != null) {
- if (temp._title == null) return false;
- else if (!(this._title.equals(temp._title)))
- return false;
- }
- else if (temp._title != null)
- return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- else if (!(this._modifiable.equals(temp._modifiable)))
- return false;
- }
- else if (temp._modifiable != 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()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return String
- * @return the value of field 'modifiable'.
- */
- public java.lang.String getModifiable()
- {
- return this._modifiable;
- } //-- java.lang.String getModifiable()
-
- /**
- * Returns the value of field 'title'.
- *
- * @return String
- * @return the value of field 'title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- } //-- java.lang.String getTitle()
-
- /**
- * 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)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(java.lang.String modifiable)
- {
- this._modifiable = modifiable;
- } //-- void setModifiable(java.lang.String)
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(java.lang.String title)
- {
- this._title = title;
- } //-- void setTitle(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Newick
- */
- public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader);
- } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class NewickDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class NewickDescriptor 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 NewickDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "newick";
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.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
- {
- Newick target = (Newick) object;
- return target.getContent();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Newick target = (Newick) 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
-
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Newick target = (Newick) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Newick target = (Newick) object;
- target.setTitle( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- 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
- {
- Newick target = (Newick) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Newick target = (Newick) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _modifiable
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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
- {
- Newick target = (Newick) object;
- return target.getModifiable();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Newick target = (Newick) object;
- target.setModifiable( (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: _modifiable
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- } //-- org.vamsas.objects.core.NewickDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return null;
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.Newick.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Param.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Param extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * The type specifies how the property will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- */\r
- private java.lang.String _type;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Param() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Param()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Param) {\r
- \r
- Param temp = (Param)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Param\r
- */\r
- public static org.vamsas.objects.core.Param unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Param) Unmarshaller.unmarshal(org.vamsas.objects.core.Param.class, reader);\r
- } //-- org.vamsas.objects.core.Param unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class ParamDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class ParamDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public ParamDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "param";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.ParamDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Param.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * a position within the associated object's coordinate system\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pos extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _i\r
- */\r
- private int _i;\r
-\r
- /**\r
- * keeps track of state for field: _i\r
- */\r
- private boolean _has_i;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Pos() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Pos()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteI\r
- * \r
- */\r
- public void deleteI()\r
- {\r
- this._has_i= false;\r
- } //-- void deleteI() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Pos) {\r
- \r
- Pos temp = (Pos)obj;\r
- if (this._i != temp._i)\r
- return false;\r
- if (this._has_i != temp._has_i)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'i'.\r
- * \r
- * @return int\r
- * @return the value of field 'i'.\r
- */\r
- public int getI()\r
- {\r
- return this._i;\r
- } //-- int getI() \r
-\r
- /**\r
- * Method hasI\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasI()\r
- {\r
- return this._has_i;\r
- } //-- boolean hasI() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'i'.\r
- * \r
- * @param i the value of field 'i'.\r
- */\r
- public void setI(int i)\r
- {\r
- this._i = i;\r
- this._has_i = true;\r
- } //-- void setI(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Pos\r
- */\r
- public static org.vamsas.objects.core.Pos unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Pos) Unmarshaller.unmarshal(org.vamsas.objects.core.Pos.class, reader);\r
- } //-- org.vamsas.objects.core.Pos unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class PosDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PosDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public PosDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "pos";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _i\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_i", "i", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Pos target = (Pos) object;\r
- if(!target.hasI())\r
- return null;\r
- return new java.lang.Integer(target.getI());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Pos target = (Pos) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setI( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _i\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.PosDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Pos.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Property.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Property extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * The type specifies how the property will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- */\r
- private java.lang.String _type;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Property() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Property()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Property) {\r
- \r
- Property temp = (Property)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Property\r
- */\r
- public static org.vamsas.objects.core.Property unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Property) Unmarshaller.unmarshal(org.vamsas.objects.core.Property.class, reader);\r
- } //-- org.vamsas.objects.core.Property unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class PropertyDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public PropertyDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "property";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.PropertyDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Property.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Provenance.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Provenance.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class Provenance extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _entryList
- */
- private java.util.Vector _entryList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Provenance()
- {
- super();
- _entryList = new Vector();
- } //-- org.vamsas.objects.core.Provenance()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addEntry
- *
- *
- *
- * @param vEntry
- */
- public void addEntry(org.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- _entryList.addElement(vEntry);
- } //-- void addEntry(org.vamsas.objects.core.Entry)
-
- /**
- * Method addEntry
- *
- *
- *
- * @param index
- * @param vEntry
- */
- public void addEntry(int index, org.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- _entryList.insertElementAt(vEntry, index);
- } //-- void addEntry(int, org.vamsas.objects.core.Entry)
-
- /**
- * Method enumerateEntry
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateEntry()
- {
- return _entryList.elements();
- } //-- java.util.Enumeration enumerateEntry()
-
- /**
- * 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._entryList != null) {
- if (temp._entryList == null) return false;
- else if (!(this._entryList.equals(temp._entryList)))
- return false;
- }
- else if (temp._entryList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getEntry
- *
- *
- *
- * @param index
- * @return Entry
- */
- public org.vamsas.objects.core.Entry getEntry(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _entryList.size())) {
- throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
- } //-- org.vamsas.objects.core.Entry getEntry(int)
-
- /**
- * Method getEntry
- *
- *
- *
- * @return Entry
- */
- public org.vamsas.objects.core.Entry[] getEntry()
- {
- int size = _entryList.size();
- org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Entry[] getEntry()
-
- /**
- * Method getEntryCount
- *
- *
- *
- * @return int
- */
- public int getEntryCount()
- {
- return _entryList.size();
- } //-- int getEntryCount()
-
- /**
- * 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 removeAllEntry
- *
- */
- public void removeAllEntry()
- {
- _entryList.removeAllElements();
- } //-- void removeAllEntry()
-
- /**
- * Method removeEntry
- *
- *
- *
- * @param index
- * @return Entry
- */
- public org.vamsas.objects.core.Entry removeEntry(int index)
- {
- java.lang.Object obj = _entryList.elementAt(index);
- _entryList.removeElementAt(index);
- return (org.vamsas.objects.core.Entry) obj;
- } //-- org.vamsas.objects.core.Entry removeEntry(int)
-
- /**
- * Method setEntry
- *
- *
- *
- * @param index
- * @param vEntry
- */
- public void setEntry(int index, org.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _entryList.size())) {
- throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
- }
- _entryList.setElementAt(vEntry, index);
- } //-- void setEntry(int, org.vamsas.objects.core.Entry)
-
- /**
- * Method setEntry
- *
- *
- *
- * @param entryArray
- */
- public void setEntry(org.vamsas.objects.core.Entry[] entryArray)
- {
- //-- copy array
- _entryList.removeAllElements();
- for (int i = 0; i < entryArray.length; i++) {
- _entryList.addElement(entryArray[i]);
- }
- } //-- void setEntry(org.vamsas.objects.core.Entry)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Provenance
- */
- public static org.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader);
- } //-- org.vamsas.objects.core.Provenance unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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();
- 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
-
- //-- _entryList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Provenance target = (Provenance) object;
- return target.getEntry();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Provenance target = (Provenance) object;
- target.addEntry( (org.vamsas.objects.core.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.objects.core.Entry();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _entryList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Annotation for a rangeSpec - values can be attached for the\r
- * whole\r
- * specification, and to each position within the spec. following\r
- * the orientation\r
- * specified by the ordered set of rangeSpec (pos, seg) elements. \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeAnnotation extends org.vamsas.objects.core.RangeType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Primary Key for vamsas object referencing\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _modifiable\r
- */\r
- private java.lang.String _modifiable;\r
-\r
- /**\r
- * Annotation with the same non-empty group name are grouped\r
- * together \r
- */\r
- private java.lang.String _group = "";\r
-\r
- /**\r
- * A Das Feature has both a type and a Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Short, meaningful name for the annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Human readable description of the annotation\r
- * \r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * TODO: specify this - we have considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Annotation Element position maps to ordered positions\r
- * defined by the sequence of rangeType pos positions or\r
- * concatenated\r
- * seg start/end segments. \r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Ordered set of optionally named float values for the\r
- * whole annotation \r
- */\r
- private java.util.Vector _scoreList;\r
-\r
- /**\r
- * Field _linkList\r
- */\r
- private java.util.Vector _linkList;\r
-\r
- /**\r
- * Note:These are mutable so an application should check\r
- * them each time. \r
- */\r
- private java.util.Vector _propertyList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeAnnotation() \r
- {\r
- super();\r
- setGroup("");\r
- _annotationElementList = new Vector();\r
- _scoreList = new Vector();\r
- _linkList = new Vector();\r
- _propertyList = new Vector();\r
- } //-- org.vamsas.objects.core.RangeAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method addLink\r
- * \r
- * \r
- * \r
- * @param vLink\r
- */\r
- public void addLink(org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.addElement(vLink);\r
- } //-- void addLink(org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method addLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- */\r
- public void addLink(int index, org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.insertElementAt(vLink, index);\r
- } //-- void addLink(int, org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param vProperty\r
- */\r
- public void addProperty(org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.addElement(vProperty);\r
- } //-- void addProperty(org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.insertElementAt(vProperty, index);\r
- } //-- void addProperty(int, org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method addScore\r
- * \r
- * \r
- * \r
- * @param vScore\r
- */\r
- public void addScore(org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.addElement(vScore);\r
- } //-- void addScore(org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method addScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- */\r
- public void addScore(int index, org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.insertElementAt(vScore, index);\r
- } //-- void addScore(int, org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
-\r
- /**\r
- * Method enumerateLink\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateLink()\r
- {\r
- return _linkList.elements();\r
- } //-- java.util.Enumeration enumerateLink() \r
-\r
- /**\r
- * Method enumerateProperty\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return _propertyList.elements();\r
- } //-- java.util.Enumeration enumerateProperty() \r
-\r
- /**\r
- * Method enumerateScore\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateScore()\r
- {\r
- return _scoreList.elements();\r
- } //-- java.util.Enumeration enumerateScore() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof RangeAnnotation) {\r
- \r
- RangeAnnotation temp = (RangeAnnotation)obj;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
- }\r
- else if (temp._id != null)\r
- return false;\r
- if (this._modifiable != null) {\r
- if (temp._modifiable == null) return false;\r
- else if (!(this._modifiable.equals(temp._modifiable))) \r
- return false;\r
- }\r
- else if (temp._modifiable != null)\r
- return false;\r
- if (this._group != null) {\r
- if (temp._group == null) return false;\r
- else if (!(this._group.equals(temp._group))) \r
- return false;\r
- }\r
- else if (temp._group != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- if (this._label != null) {\r
- if (temp._label == null) return false;\r
- else if (!(this._label.equals(temp._label))) \r
- return false;\r
- }\r
- else if (temp._label != null)\r
- return false;\r
- if (this._description != null) {\r
- if (temp._description == null) return false;\r
- else if (!(this._description.equals(temp._description))) \r
- return false;\r
- }\r
- else if (temp._description != null)\r
- return false;\r
- if (this._status != null) {\r
- if (temp._status == null) return false;\r
- else if (!(this._status.equals(temp._status))) \r
- return false;\r
- }\r
- else if (temp._status != null)\r
- return false;\r
- if (this._annotationElementList != null) {\r
- if (temp._annotationElementList == null) return false;\r
- else if (!(this._annotationElementList.equals(temp._annotationElementList))) \r
- return false;\r
- }\r
- else if (temp._annotationElementList != null)\r
- return false;\r
- if (this._scoreList != null) {\r
- if (temp._scoreList == null) return false;\r
- else if (!(this._scoreList.equals(temp._scoreList))) \r
- return false;\r
- }\r
- else if (temp._scoreList != null)\r
- return false;\r
- if (this._linkList != null) {\r
- if (temp._linkList == null) return false;\r
- else if (!(this._linkList.equals(temp._linkList))) \r
- return false;\r
- }\r
- else if (temp._linkList != null)\r
- return false;\r
- if (this._propertyList != null) {\r
- if (temp._propertyList == null) return false;\r
- else if (!(this._propertyList.equals(temp._propertyList))) \r
- return false;\r
- }\r
- else if (temp._propertyList != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() \r
-\r
- /**\r
- * Method getAnnotationElementCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
-\r
- /**\r
- * Returns the value of field 'description'. The field\r
- * 'description' has the following description: Human readable\r
- * description of the annotation\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'group'. The field 'group' has\r
- * the following description: Annotation with the same\r
- * non-empty group name are grouped\r
- * together \r
- * \r
- * @return String\r
- * @return the value of field 'group'.\r
- */\r
- public java.lang.String getGroup()\r
- {\r
- return this._group;\r
- } //-- java.lang.String getGroup() \r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'label'. The field 'label' has\r
- * the following description: Short, meaningful name for the\r
- * annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel()\r
- {\r
- return this._label;\r
- } //-- java.lang.String getLabel() \r
-\r
- /**\r
- * Method getLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link getLink(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Link getLink(int) \r
-\r
- /**\r
- * Method getLink\r
- * \r
- * \r
- * \r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link[] getLink()\r
- {\r
- int size = _linkList.size();\r
- org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Link[] getLink() \r
-\r
- /**\r
- * Method getLinkCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getLinkCount()\r
- {\r
- return _linkList.size();\r
- } //-- int getLinkCount() \r
-\r
- /**\r
- * Returns the value of field 'modifiable'.\r
- * \r
- * @return String\r
- * @return the value of field 'modifiable'.\r
- */\r
- public java.lang.String getModifiable()\r
- {\r
- return this._modifiable;\r
- } //-- java.lang.String getModifiable() \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property getProperty(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Property getProperty(int) \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property[] getProperty()\r
- {\r
- int size = _propertyList.size();\r
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Property[] getProperty() \r
-\r
- /**\r
- * Method getPropertyCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPropertyCount()\r
- {\r
- return _propertyList.size();\r
- } //-- int getPropertyCount() \r
-\r
- /**\r
- * Method getScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score getScore(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Score getScore(int) \r
-\r
- /**\r
- * Method getScore\r
- * \r
- * \r
- * \r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score[] getScore()\r
- {\r
- int size = _scoreList.size();\r
- org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Score[] getScore() \r
-\r
- /**\r
- * Method getScoreCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getScoreCount()\r
- {\r
- return _scoreList.size();\r
- } //-- int getScoreCount() \r
-\r
- /**\r
- * Returns the value of field 'status'. The field 'status' has\r
- * the following description: TODO: specify this - we have\r
- * considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @return String\r
- * @return the value of field 'status'.\r
- */\r
- public java.lang.String getStatus()\r
- {\r
- return this._status;\r
- } //-- java.lang.String getStatus() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: A Das Feature has both a type and a\r
- * Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllAnnotationElement\r
- * \r
- */\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
-\r
- /**\r
- * Method removeAllLink\r
- * \r
- */\r
- public void removeAllLink()\r
- {\r
- _linkList.removeAllElements();\r
- } //-- void removeAllLink() \r
-\r
- /**\r
- * Method removeAllProperty\r
- * \r
- */\r
- public void removeAllProperty()\r
- {\r
- _propertyList.removeAllElements();\r
- } //-- void removeAllProperty() \r
-\r
- /**\r
- * Method removeAllScore\r
- * \r
- */\r
- public void removeAllScore()\r
- {\r
- _scoreList.removeAllElements();\r
- } //-- void removeAllScore() \r
-\r
- /**\r
- * Method removeAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
- return (org.vamsas.objects.core.AnnotationElement) obj;\r
- } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) \r
-\r
- /**\r
- * Method removeLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link removeLink(int index)\r
- {\r
- java.lang.Object obj = _linkList.elementAt(index);\r
- _linkList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Link) obj;\r
- } //-- org.vamsas.objects.core.Link removeLink(int) \r
-\r
- /**\r
- * Method removeProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property removeProperty(int index)\r
- {\r
- java.lang.Object obj = _propertyList.elementAt(index);\r
- _propertyList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Property) obj;\r
- } //-- org.vamsas.objects.core.Property removeProperty(int) \r
-\r
- /**\r
- * Method removeScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score removeScore(int index)\r
- {\r
- java.lang.Object obj = _scoreList.elementAt(index);\r
- _scoreList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Score) obj;\r
- } //-- org.vamsas.objects.core.Score removeScore(int) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
- }\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)\r
- {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
- }\r
- } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Sets the value of field 'description'. The field\r
- * 'description' has the following description: Human readable\r
- * description of the annotation\r
- * \r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'group'. The field 'group' has the\r
- * following description: Annotation with the same non-empty\r
- * group name are grouped\r
- * together \r
- * \r
- * @param group the value of field 'group'.\r
- */\r
- public void setGroup(java.lang.String group)\r
- {\r
- this._group = group;\r
- } //-- void setGroup(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'label'. The field 'label' has the\r
- * following description: Short, meaningful name for the\r
- * annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(java.lang.String label)\r
- {\r
- this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
-\r
- /**\r
- * Method setLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- */\r
- public void setLink(int index, org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
- }\r
- _linkList.setElementAt(vLink, index);\r
- } //-- void setLink(int, org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method setLink\r
- * \r
- * \r
- * \r
- * @param linkArray\r
- */\r
- public void setLink(org.vamsas.objects.core.Link[] linkArray)\r
- {\r
- //-- copy array\r
- _linkList.removeAllElements();\r
- for (int i = 0; i < linkArray.length; i++) {\r
- _linkList.addElement(linkArray[i]);\r
- }\r
- } //-- void setLink(org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Sets the value of field 'modifiable'.\r
- * \r
- * @param modifiable the value of field 'modifiable'.\r
- */\r
- public void setModifiable(java.lang.String modifiable)\r
- {\r
- this._modifiable = modifiable;\r
- } //-- void setModifiable(java.lang.String) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
- }\r
- _propertyList.setElementAt(vProperty, index);\r
- } //-- void setProperty(int, org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param propertyArray\r
- */\r
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)\r
- {\r
- //-- copy array\r
- _propertyList.removeAllElements();\r
- for (int i = 0; i < propertyArray.length; i++) {\r
- _propertyList.addElement(propertyArray[i]);\r
- }\r
- } //-- void setProperty(org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method setScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- */\r
- public void setScore(int index, org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
- }\r
- _scoreList.setElementAt(vScore, index);\r
- } //-- void setScore(int, org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method setScore\r
- * \r
- * \r
- * \r
- * @param scoreArray\r
- */\r
- public void setScore(org.vamsas.objects.core.Score[] scoreArray)\r
- {\r
- //-- copy array\r
- _scoreList.removeAllElements();\r
- for (int i = 0; i < scoreArray.length; i++) {\r
- _scoreList.addElement(scoreArray[i]);\r
- }\r
- } //-- void setScore(org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Sets the value of field 'status'. The field 'status' has the\r
- * following description: TODO: specify this - we have\r
- * considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @param status the value of field 'status'.\r
- */\r
- public void setStatus(java.lang.String status)\r
- {\r
- this._status = status;\r
- } //-- void setStatus(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: A Das Feature has both a type and a\r
- * Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class RangeAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeAnnotationDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "rangeAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
- this.identity = desc;\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getId();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setId( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _modifiable\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getModifiable();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setModifiable( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _modifiable\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _group\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_group", "group", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getGroup();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setGroup( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _group\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _label\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getLabel();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setLabel( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _label\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getDescription();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setDescription( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _status\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getStatus();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setStatus( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _status\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _annotationElementList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getAnnotationElement();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.AnnotationElement();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _annotationElementList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _scoreList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Score.class, "_scoreList", "score", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getScore();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addScore( (org.vamsas.objects.core.Score) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Score();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _scoreList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _linkList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getLink();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addLink( (org.vamsas.objects.core.Link) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Link();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _linkList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _propertyList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getProperty();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addProperty( (org.vamsas.objects.core.Property) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Property();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _propertyList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.RangeAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.RangeAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-\r
-/**\r
- * Specify an ordered set of positions and/or regions on the\r
- * principle\r
- * dimension of some associated vamsas object Keeping to jaxb-1.0\r
- * specification for the moment - this choice should\r
- * become a substitution group when we use jaxb-2.0 capable\r
- * bindings\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public abstract class RangeType extends uk.ac.vamsas.clientnt.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Internal choice value storage\r
- */\r
- private java.lang.Object _choiceValue;\r
-\r
- /**\r
- * a position within the associated object's coordinate system\r
- * \r
- */\r
- private java.util.Vector _posList;\r
-\r
- /**\r
- * a region from start to end, with flag for inclusivity of\r
- * terminii \r
- */\r
- private java.util.Vector _segList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeType() \r
- {\r
- super();\r
- _posList = new Vector();\r
- _segList = new Vector();\r
- } //-- uk.ac.vamsas.objects.core.RangeType()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addPos\r
- * \r
- * \r
- * \r
- * @param vPos\r
- */\r
- public void addPos(uk.ac.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _posList.addElement(vPos);\r
- } //-- void addPos(uk.ac.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method addPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPos\r
- */\r
- public void addPos(int index, uk.ac.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _posList.insertElementAt(vPos, index);\r
- } //-- void addPos(int, uk.ac.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method addSeg\r
- * \r
- * \r
- * \r
- * @param vSeg\r
- */\r
- public void addSeg(uk.ac.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _segList.addElement(vSeg);\r
- } //-- void addSeg(uk.ac.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method addSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeg\r
- */\r
- public void addSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _segList.insertElementAt(vSeg, index);\r
- } //-- void addSeg(int, uk.ac.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method enumeratePos\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePos()\r
- {\r
- return _posList.elements();\r
- } //-- java.util.Enumeration enumeratePos() \r
-\r
- /**\r
- * Method enumerateSeg\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSeg()\r
- {\r
- return _segList.elements();\r
- } //-- java.util.Enumeration enumerateSeg() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof RangeType) {\r
- \r
- RangeType temp = (RangeType)obj;\r
- if (this._choiceValue != null) {\r
- if (temp._choiceValue == null) return false;\r
- else if (!(this._choiceValue.equals(temp._choiceValue))) \r
- return false;\r
- }\r
- else if (temp._choiceValue != null)\r
- return false;\r
- if (this._posList != null) {\r
- if (temp._posList == null) return false;\r
- else if (!(this._posList.equals(temp._posList))) \r
- return false;\r
- }\r
- else if (temp._posList != null)\r
- return false;\r
- if (this._segList != null) {\r
- if (temp._segList == null) return false;\r
- else if (!(this._segList.equals(temp._segList))) \r
- return false;\r
- }\r
- else if (temp._segList != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'choiceValue'. The field\r
- * 'choiceValue' has the following description: Internal choice\r
- * value storage\r
- * \r
- * @return Object\r
- * @return the value of field 'choiceValue'.\r
- */\r
- public java.lang.Object getChoiceValue()\r
- {\r
- return this._choiceValue;\r
- } //-- java.lang.Object getChoiceValue() \r
-\r
- /**\r
- * Method getPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pos\r
- */\r
- public uk.ac.vamsas.objects.core.Pos getPos(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _posList.size())) {\r
- throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.Pos getPos(int) \r
-\r
- /**\r
- * Method getPos\r
- * \r
- * \r
- * \r
- * @return Pos\r
- */\r
- public uk.ac.vamsas.objects.core.Pos[] getPos()\r
- {\r
- int size = _posList.size();\r
- uk.ac.vamsas.objects.core.Pos[] mArray = new uk.ac.vamsas.objects.core.Pos[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.Pos[] getPos() \r
-\r
- /**\r
- * Method getPosCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPosCount()\r
- {\r
- return _posList.size();\r
- } //-- int getPosCount() \r
-\r
- /**\r
- * Method getSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Seg\r
- */\r
- public uk.ac.vamsas.objects.core.Seg getSeg(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _segList.size())) {\r
- throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.Seg getSeg(int) \r
-\r
- /**\r
- * Method getSeg\r
- * \r
- * \r
- * \r
- * @return Seg\r
- */\r
- public uk.ac.vamsas.objects.core.Seg[] getSeg()\r
- {\r
- int size = _segList.size();\r
- uk.ac.vamsas.objects.core.Seg[] mArray = new uk.ac.vamsas.objects.core.Seg[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.Seg[] getSeg() \r
-\r
- /**\r
- * Method getSegCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSegCount()\r
- {\r
- return _segList.size();\r
- } //-- int getSegCount() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method removeAllPos\r
- * \r
- */\r
- public void removeAllPos()\r
- {\r
- _posList.removeAllElements();\r
- } //-- void removeAllPos() \r
-\r
- /**\r
- * Method removeAllSeg\r
- * \r
- */\r
- public void removeAllSeg()\r
- {\r
- _segList.removeAllElements();\r
- } //-- void removeAllSeg() \r
-\r
- /**\r
- * Method removePos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pos\r
- */\r
- public uk.ac.vamsas.objects.core.Pos removePos(int index)\r
- {\r
- java.lang.Object obj = _posList.elementAt(index);\r
- _posList.removeElementAt(index);\r
- return (uk.ac.vamsas.objects.core.Pos) obj;\r
- } //-- uk.ac.vamsas.objects.core.Pos removePos(int) \r
-\r
- /**\r
- * Method removeSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Seg\r
- */\r
- public uk.ac.vamsas.objects.core.Seg removeSeg(int index)\r
- {\r
- java.lang.Object obj = _segList.elementAt(index);\r
- _segList.removeElementAt(index);\r
- return (uk.ac.vamsas.objects.core.Seg) obj;\r
- } //-- uk.ac.vamsas.objects.core.Seg removeSeg(int) \r
-\r
- /**\r
- * Method setPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPos\r
- */\r
- public void setPos(int index, uk.ac.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _posList.size())) {\r
- throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
- }\r
- _posList.setElementAt(vPos, index);\r
- } //-- void setPos(int, uk.ac.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method setPos\r
- * \r
- * \r
- * \r
- * @param posArray\r
- */\r
- public void setPos(uk.ac.vamsas.objects.core.Pos[] posArray)\r
- {\r
- //-- copy array\r
- _posList.removeAllElements();\r
- for (int i = 0; i < posArray.length; i++) {\r
- _posList.addElement(posArray[i]);\r
- }\r
- } //-- void setPos(uk.ac.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method setSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeg\r
- */\r
- public void setSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _segList.size())) {\r
- throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
- }\r
- _segList.setElementAt(vSeg, index);\r
- } //-- void setSeg(int, uk.ac.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method setSeg\r
- * \r
- * \r
- * \r
- * @param segArray\r
- */\r
- public void setSeg(uk.ac.vamsas.objects.core.Seg[] segArray)\r
- {\r
- //-- copy array\r
- _segList.removeAllElements();\r
- for (int i = 0; i < segArray.length; i++) {\r
- _segList.addElement(segArray[i]);\r
- }\r
- } //-- void setSeg(uk.ac.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class RangeTypeDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeTypeDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "rangeType";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- initialize element descriptors\r
- \r
- //-- _posList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Pos.class, "_posList", "pos", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeType target = (RangeType) object;\r
- return target.getPos();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeType target = (RangeType) object;\r
- target.addPos( (org.vamsas.objects.core.Pos) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _posList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _segList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Seg.class, "_segList", "seg", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeType target = (RangeType) object;\r
- return target.getSeg();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeType target = (RangeType) object;\r
- target.addSeg( (org.vamsas.objects.core.Seg) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _segList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.RangeTypeDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.RangeType.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Ordered set of optionally named float values for the\r
- * whole annotation \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Score extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private float _content;\r
-\r
- /**\r
- * keeps track of state for field: _content\r
- */\r
- private boolean _has_content;\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name = "score";\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Score() \r
- {\r
- super();\r
- setName("score");\r
- } //-- org.vamsas.objects.core.Score()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteContent\r
- * \r
- */\r
- public void deleteContent()\r
- {\r
- this._has_content= false;\r
- } //-- void deleteContent() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Score) {\r
- \r
- Score temp = (Score)obj;\r
- if (this._content != temp._content)\r
- return false;\r
- if (this._has_content != temp._has_content)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return float\r
- * @return the value of field 'content'.\r
- */\r
- public float getContent()\r
- {\r
- return this._content;\r
- } //-- float getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Method hasContent\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasContent()\r
- {\r
- return this._has_content;\r
- } //-- boolean hasContent() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(float content)\r
- {\r
- this._content = content;\r
- this._has_content = true;\r
- } //-- void setContent(float) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Score\r
- */\r
- public static org.vamsas.objects.core.Score unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Score) Unmarshaller.unmarshal(org.vamsas.objects.core.Score.class, reader);\r
- } //-- org.vamsas.objects.core.Score unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class ScoreDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class ScoreDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public ScoreDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "score";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Score target = (Score) object;\r
- if(!target.hasContent())\r
- return null;\r
- return new java.lang.Float(target.getContent());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Score target = (Score) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteContent();\r
- return;\r
- }\r
- target.setContent( ((java.lang.Float)value).floatValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- FloatValidator typeValidator = new FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Score target = (Score) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Score target = (Score) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.ScoreDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Score.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * a region from start to end, with flag for inclusivity of\r
- * terminii \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Seg extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _start\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * when false, a consecutive range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- */\r
- private boolean _inclusive;\r
-\r
- /**\r
- * keeps track of state for field: _inclusive\r
- */\r
- private boolean _has_inclusive;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Seg() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Seg()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteInclusive\r
- * \r
- */\r
- public void deleteInclusive()\r
- {\r
- this._has_inclusive= false;\r
- } //-- void deleteInclusive() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Seg) {\r
- \r
- Seg temp = (Seg)obj;\r
- if (this._start != temp._start)\r
- return false;\r
- if (this._has_start != temp._has_start)\r
- return false;\r
- if (this._end != temp._end)\r
- return false;\r
- if (this._has_end != temp._has_end)\r
- return false;\r
- if (this._inclusive != temp._inclusive)\r
- return false;\r
- if (this._has_inclusive != temp._has_inclusive)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd() \r
-\r
- /**\r
- * Returns the value of field 'inclusive'. The field\r
- * 'inclusive' has the following description: when false, a\r
- * consecutive range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- * \r
- * @return boolean\r
- * @return the value of field 'inclusive'.\r
- */\r
- public boolean getInclusive()\r
- {\r
- return this._inclusive;\r
- } //-- boolean getInclusive() \r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart() \r
-\r
- /**\r
- * Method hasEnd\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd() \r
-\r
- /**\r
- * Method hasInclusive\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasInclusive()\r
- {\r
- return this._has_inclusive;\r
- } //-- boolean hasInclusive() \r
-\r
- /**\r
- * Method hasStart\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int) \r
-\r
- /**\r
- * Sets the value of field 'inclusive'. The field 'inclusive'\r
- * has the following description: when false, a consecutive\r
- * range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- * \r
- * @param inclusive the value of field 'inclusive'.\r
- */\r
- public void setInclusive(boolean inclusive)\r
- {\r
- this._inclusive = inclusive;\r
- this._has_inclusive = true;\r
- } //-- void setInclusive(boolean) \r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Seg\r
- */\r
- public static org.vamsas.objects.core.Seg unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Seg) Unmarshaller.unmarshal(org.vamsas.objects.core.Seg.class, reader);\r
- } //-- org.vamsas.objects.core.Seg unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class SegDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SegDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SegDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "seg";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasStart())\r
- return null;\r
- return new java.lang.Integer(target.getStart());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setStart( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasEnd())\r
- return null;\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setEnd( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _inclusive\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_inclusive", "inclusive", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasInclusive())\r
- return null;\r
- return (target.getInclusive() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setInclusive( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _inclusive\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.SegDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Seg.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Sequence.
- *
- * @version $Revision$ $Date$
- */
-public class Sequence extends org.vamsas.objects.core.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * symbol class for sequence
- *
- */
- private java.lang.String _dictionary;
-
- /**
- * Store a list of database references
- * for this sequence record - with optional mapping
- * from database sequence to the given sequence record
- */
- private java.util.Vector _dbRefList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence()
- {
- super();
- _dbRefList = new Vector();
- } //-- org.vamsas.objects.core.Sequence()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addDbRef
- *
- *
- *
- * @param vDbRef
- */
- public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.addElement(vDbRef);
- } //-- void addDbRef(org.vamsas.objects.core.DbRef)
-
- /**
- * Method addDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.insertElementAt(vDbRef, index);
- } //-- void addDbRef(int, org.vamsas.objects.core.DbRef)
-
- /**
- * 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 Sequence) {
-
- Sequence temp = (Sequence)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._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._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.objects.core.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.objects.core.DbRef) _dbRefList.elementAt(index);
- } //-- org.vamsas.objects.core.DbRef getDbRef(int)
-
- /**
- * Method getDbRef
- *
- *
- *
- * @return DbRef
- */
- public org.vamsas.objects.core.DbRef[] getDbRef()
- {
- int size = _dbRefList.size();
- org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.DbRef[] getDbRef()
-
- /**
- * Method getDbRefCount
- *
- *
- *
- * @return int
- */
- public int getDbRefCount()
- {
- return _dbRefList.size();
- } //-- int getDbRefCount()
-
- /**
- * Returns the value of field 'dictionary'. The field
- * 'dictionary' has the following description: symbol class for
- * sequence
- *
- *
- * @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'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @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)
-
- /**
- * Method removeAllDbRef
- *
- */
- public void removeAllDbRef()
- {
- _dbRefList.removeAllElements();
- } //-- void removeAllDbRef()
-
- /**
- * Method removeDbRef
- *
- *
- *
- * @param index
- * @return DbRef
- */
- public org.vamsas.objects.core.DbRef removeDbRef(int index)
- {
- java.lang.Object obj = _dbRefList.elementAt(index);
- _dbRefList.removeElementAt(index);
- return (org.vamsas.objects.core.DbRef) obj;
- } //-- org.vamsas.objects.core.DbRef removeDbRef(int)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void setDbRef(int index, org.vamsas.objects.core.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.objects.core.DbRef)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param dbRefArray
- */
- public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
- {
- //-- copy array
- _dbRefList.removeAllElements();
- for (int i = 0; i < dbRefArray.length; i++) {
- _dbRefList.addElement(dbRefArray[i]);
- }
- } //-- void setDbRef(org.vamsas.objects.core.DbRef)
-
- /**
- * Sets the value of field 'dictionary'. The field 'dictionary'
- * has the following description: symbol class for sequence
- *
- *
- * @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'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @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.objects.core.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader);
- } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class SequenceDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceDescriptor extends org.vamsas.objects.core.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.objects.core.SequenceTypeDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "Sequence";
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- 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.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dictionary
- 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);
- //-- initialize element descriptors
-
- //-- _dbRefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getDbRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.addDbRef( (org.vamsas.objects.core.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.objects.core.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.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:SequenceType.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class SequenceType.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class SequenceType extends uk.ac.vamsas.client.Vobject
-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 _description
- */
- private java.lang.String _description;
-
- /**
- * additional typed properties
- */
- private java.util.Vector _propertyList;
-
- /**
- * Field _mappingList
- */
- private java.util.Vector _mappingList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType()
- {
- super();
- _propertyList = new Vector();
- _mappingList = new Vector();
- } //-- org.vamsas.objects.core.SequenceType()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addMapping
- *
- *
- *
- * @param vMapping
- */
- public void addMapping(org.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- _mappingList.addElement(vMapping);
- } //-- void addMapping(org.vamsas.objects.core.Mapping)
-
- /**
- * Method addMapping
- *
- *
- *
- * @param index
- * @param vMapping
- */
- public void addMapping(int index, org.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- _mappingList.insertElementAt(vMapping, index);
- } //-- void addMapping(int, org.vamsas.objects.core.Mapping)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method deleteStart
- *
- */
- public void deleteStart()
- {
- this._has_start= false;
- } //-- void deleteStart()
-
- /**
- * Method enumerateMapping
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateMapping()
- {
- return _mappingList.elements();
- } //-- java.util.Enumeration enumerateMapping()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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._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._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != null)
- return false;
- if (this._mappingList != null) {
- if (temp._mappingList == null) return false;
- else if (!(this._mappingList.equals(temp._mappingList)))
- return false;
- }
- else if (temp._mappingList != null)
- 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 'end'.
- *
- * @return int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- int getEnd()
-
- /**
- * Method getMapping
- *
- *
- *
- * @param index
- * @return Mapping
- */
- public org.vamsas.objects.core.Mapping getMapping(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mappingList.size())) {
- throw new IndexOutOfBoundsException("getMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
- } //-- org.vamsas.objects.core.Mapping getMapping(int)
-
- /**
- * Method getMapping
- *
- *
- *
- * @return Mapping
- */
- public org.vamsas.objects.core.Mapping[] getMapping()
- {
- int size = _mappingList.size();
- org.vamsas.objects.core.Mapping[] mArray = new org.vamsas.objects.core.Mapping[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Mapping[] getMapping()
-
- /**
- * Method getMappingCount
- *
- *
- *
- * @return int
- */
- public int getMappingCount()
- {
- return _mappingList.size();
- } //-- int getMappingCount()
-
- /**
- * 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()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * 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 removeAllMapping
- *
- */
- public void removeAllMapping()
- {
- _mappingList.removeAllElements();
- } //-- void removeAllMapping()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeMapping
- *
- *
- *
- * @param index
- * @return Mapping
- */
- public org.vamsas.objects.core.Mapping removeMapping(int index)
- {
- java.lang.Object obj = _mappingList.elementAt(index);
- _mappingList.removeElementAt(index);
- return (org.vamsas.objects.core.Mapping) obj;
- } //-- org.vamsas.objects.core.Mapping removeMapping(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * 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(int end)
- {
- this._end = end;
- this._has_end = true;
- } //-- void setEnd(int)
-
- /**
- * Method setMapping
- *
- *
- *
- * @param index
- * @param vMapping
- */
- public void setMapping(int index, org.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mappingList.size())) {
- throw new IndexOutOfBoundsException("setMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
- }
- _mappingList.setElementAt(vMapping, index);
- } //-- void setMapping(int, org.vamsas.objects.core.Mapping)
-
- /**
- * Method setMapping
- *
- *
- *
- * @param mappingArray
- */
- public void setMapping(org.vamsas.objects.core.Mapping[] mappingArray)
- {
- //-- copy array
- _mappingList.removeAllElements();
- for (int i = 0; i < mappingArray.length; i++) {
- _mappingList.addElement(mappingArray[i]);
- }
- } //-- void setMapping(org.vamsas.objects.core.Mapping)
-
- /**
- * 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)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * 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.objects.core.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader);
- } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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);
- //-- _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
- {
- SequenceType target = (SequenceType) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setDescription( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.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);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.addProperty( (org.vamsas.objects.core.Property) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _mappingList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Mapping.class, "_mappingList", "mapping", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getMapping();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.addMapping( (org.vamsas.objects.core.Mapping) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Mapping();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _mappingList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Tree.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Tree.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class Tree extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable
- */
- private java.lang.String _modifiable;
-
- /**
- * Field _title
- */
- private java.lang.String _title;
-
- /**
- * Field _newickList
- */
- private java.util.Vector _newickList;
-
- /**
- * Field _propertyList
- */
- private java.util.Vector _propertyList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree()
- {
- super();
- _newickList = new Vector();
- _propertyList = new Vector();
- } //-- org.vamsas.objects.core.Tree()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addNewick
- *
- *
- *
- * @param vNewick
- */
- public void addNewick(org.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException
- {
- _newickList.addElement(vNewick);
- } //-- void addNewick(org.vamsas.objects.core.Newick)
-
- /**
- * Method addNewick
- *
- *
- *
- * @param index
- * @param vNewick
- */
- public void addNewick(int index, org.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException
- {
- _newickList.insertElementAt(vNewick, index);
- } //-- void addNewick(int, org.vamsas.objects.core.Newick)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method enumerateNewick
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateNewick()
- {
- return _newickList.elements();
- } //-- java.util.Enumeration enumerateNewick()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- else if (!(this._modifiable.equals(temp._modifiable)))
- return false;
- }
- else if (temp._modifiable != null)
- return false;
- if (this._title != null) {
- if (temp._title == null) return false;
- else if (!(this._title.equals(temp._title)))
- return false;
- }
- else if (temp._title != null)
- return false;
- if (this._newickList != null) {
- if (temp._newickList == null) return false;
- else if (!(this._newickList.equals(temp._newickList)))
- return false;
- }
- else if (temp._newickList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
- }
- else if (temp._provenance != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return String
- * @return the value of field 'modifiable'.
- */
- public java.lang.String getModifiable()
- {
- return this._modifiable;
- } //-- java.lang.String getModifiable()
-
- /**
- * Method getNewick
- *
- *
- *
- * @param index
- * @return Newick
- */
- public org.vamsas.objects.core.Newick getNewick(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _newickList.size())) {
- throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
- } //-- org.vamsas.objects.core.Newick getNewick(int)
-
- /**
- * Method getNewick
- *
- *
- *
- * @return Newick
- */
- public org.vamsas.objects.core.Newick[] getNewick()
- {
- int size = _newickList.size();
- org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Newick[] getNewick()
-
- /**
- * Method getNewickCount
- *
- *
- *
- * @return int
- */
- public int getNewickCount()
- {
- return _newickList.size();
- } //-- int getNewickCount()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Returns the value of field 'title'.
- *
- * @return String
- * @return the value of field 'title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- } //-- java.lang.String getTitle()
-
- /**
- * 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 removeAllNewick
- *
- */
- public void removeAllNewick()
- {
- _newickList.removeAllElements();
- } //-- void removeAllNewick()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeNewick
- *
- *
- *
- * @param index
- * @return Newick
- */
- public org.vamsas.objects.core.Newick removeNewick(int index)
- {
- java.lang.Object obj = _newickList.elementAt(index);
- _newickList.removeElementAt(index);
- return (org.vamsas.objects.core.Newick) obj;
- } //-- org.vamsas.objects.core.Newick removeNewick(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(java.lang.String modifiable)
- {
- this._modifiable = modifiable;
- } //-- void setModifiable(java.lang.String)
-
- /**
- * Method setNewick
- *
- *
- *
- * @param index
- * @param vNewick
- */
- public void setNewick(int index, org.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _newickList.size())) {
- throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
- }
- _newickList.setElementAt(vNewick, index);
- } //-- void setNewick(int, org.vamsas.objects.core.Newick)
-
- /**
- * Method setNewick
- *
- *
- *
- * @param newickArray
- */
- public void setNewick(org.vamsas.objects.core.Newick[] newickArray)
- {
- //-- copy array
- _newickList.removeAllElements();
- for (int i = 0; i < newickArray.length; i++) {
- _newickList.addElement(newickArray[i]);
- }
- } //-- void setNewick(org.vamsas.objects.core.Newick)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(java.lang.String title)
- {
- this._title = title;
- } //-- void setTitle(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Tree
- */
- public static org.vamsas.objects.core.Tree unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader);
- } //-- org.vamsas.objects.core.Tree unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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
-
- //-- _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
- {
- Tree target = (Tree) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _modifiable
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getModifiable();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setModifiable( (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: _modifiable
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getTitle();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setTitle( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _newickList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getNewick();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.addNewick( (org.vamsas.objects.core.Newick) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Newick();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _newickList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _propertyList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getProperty();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.addProperty( (org.vamsas.objects.core.Property) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Property();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _propertyList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class User.
- *
- * @version $Revision$ $Date$
- */
-public class User extends org.vamsas.objects.core.AppData
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _fullname
- */
- private java.lang.String _fullname;
-
- /**
- * Field _organization
- */
- private java.lang.String _organization;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public User()
- {
- super();
- } //-- org.vamsas.objects.core.User()
-
-
- //-----------/
- //- 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 User) {
-
- User temp = (User)obj;
- if (this._fullname != null) {
- if (temp._fullname == null) return false;
- else if (!(this._fullname.equals(temp._fullname)))
- return false;
- }
- else if (temp._fullname != null)
- return false;
- if (this._organization != null) {
- if (temp._organization == null) return false;
- else if (!(this._organization.equals(temp._organization)))
- return false;
- }
- else if (temp._organization != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'fullname'.
- *
- * @return String
- * @return the value of field 'fullname'.
- */
- public java.lang.String getFullname()
- {
- return this._fullname;
- } //-- java.lang.String getFullname()
-
- /**
- * Returns the value of field 'organization'.
- *
- * @return String
- * @return the value of field 'organization'.
- */
- public java.lang.String getOrganization()
- {
- return this._organization;
- } //-- java.lang.String getOrganization()
-
- /**
- * 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 'fullname'.
- *
- * @param fullname the value of field 'fullname'.
- */
- public void setFullname(java.lang.String fullname)
- {
- this._fullname = fullname;
- } //-- void setFullname(java.lang.String)
-
- /**
- * Sets the value of field 'organization'.
- *
- * @param organization the value of field 'organization'.
- */
- public void setOrganization(java.lang.String organization)
- {
- this._organization = organization;
- } //-- void setOrganization(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return AppData
- */
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader);
- } //-- org.vamsas.objects.core.AppData 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class UserDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class UserDescriptor extends org.vamsas.objects.core.AppDataDescriptor {
-
-
- //--------------------------/
- //- 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 UserDescriptor()
- {
- super();
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "User";
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _fullname
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- User target = (User) object;
- return target.getFullname();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- User target = (User) object;
- target.setFullname( (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: _fullname
- 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);
- //-- _organization
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- User target = (User) object;
- return target.getOrganization();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- User target = (User) object;
- target.setOrganization( (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: _organization
- 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);
- //-- initialize element descriptors
-
- } //-- org.vamsas.objects.core.UserDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return super.getExtends();
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- if (identity == null)
- return super.getIdentity();
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.User.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:VAMSAS.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * contains unassociated trees and a number of analysis sets
- *
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class VAMSAS extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable
- */
- private java.lang.String _modifiable;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _dataSetList
- */
- private java.util.Vector _dataSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS()
- {
- super();
- _treeList = new Vector();
- _dataSetList = new Vector();
- } //-- org.vamsas.objects.core.VAMSAS()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addDataSet
- *
- *
- *
- * @param vDataSet
- */
- public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetList.addElement(vDataSet);
- } //-- void addDataSet(org.vamsas.objects.core.DataSet)
-
- /**
- * Method addDataSet
- *
- *
- *
- * @param index
- * @param vDataSet
- */
- public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetList.insertElementAt(vDataSet, index);
- } //-- void addDataSet(int, org.vamsas.objects.core.DataSet)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, org.vamsas.objects.core.Tree)
-
- /**
- * Method enumerateDataSet
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDataSet()
- {
- return _dataSetList.elements();
- } //-- java.util.Enumeration enumerateDataSet()
-
- /**
- * 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._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- else if (!(this._modifiable.equals(temp._modifiable)))
- return false;
- }
- else if (temp._modifiable != 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._dataSetList != null) {
- if (temp._dataSetList == null) return false;
- else if (!(this._dataSetList.equals(temp._dataSetList)))
- return false;
- }
- else if (temp._dataSetList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getDataSet
- *
- *
- *
- * @param index
- * @return DataSet
- */
- public org.vamsas.objects.core.DataSet getDataSet(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetList.size())) {
- throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
- } //-- org.vamsas.objects.core.DataSet getDataSet(int)
-
- /**
- * Method getDataSet
- *
- *
- *
- * @return DataSet
- */
- public org.vamsas.objects.core.DataSet[] getDataSet()
- {
- int size = _dataSetList.size();
- org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.DataSet[] getDataSet()
-
- /**
- * Method getDataSetCount
- *
- *
- *
- * @return int
- */
- public int getDataSetCount()
- {
- return _dataSetList.size();
- } //-- int getDataSetCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return String
- * @return the value of field 'modifiable'.
- */
- public java.lang.String getModifiable()
- {
- return this._modifiable;
- } //-- java.lang.String getModifiable()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.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.objects.core.Tree) _treeList.elementAt(index);
- } //-- org.vamsas.objects.core.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public org.vamsas.objects.core.Tree[] getTree()
- {
- int size = _treeList.size();
- org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Tree[] getTree()
-
- /**
- * 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 removeAllDataSet
- *
- */
- public void removeAllDataSet()
- {
- _dataSetList.removeAllElements();
- } //-- void removeAllDataSet()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeDataSet
- *
- *
- *
- * @param index
- * @return DataSet
- */
- public org.vamsas.objects.core.DataSet removeDataSet(int index)
- {
- java.lang.Object obj = _dataSetList.elementAt(index);
- _dataSetList.removeElementAt(index);
- return (org.vamsas.objects.core.DataSet) obj;
- } //-- org.vamsas.objects.core.DataSet removeDataSet(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (org.vamsas.objects.core.Tree) obj;
- } //-- org.vamsas.objects.core.Tree removeTree(int)
-
- /**
- * Method setDataSet
- *
- *
- *
- * @param index
- * @param vDataSet
- */
- public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetList.size())) {
- throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
- }
- _dataSetList.setElementAt(vDataSet, index);
- } //-- void setDataSet(int, org.vamsas.objects.core.DataSet)
-
- /**
- * Method setDataSet
- *
- *
- *
- * @param dataSetArray
- */
- public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
- {
- //-- copy array
- _dataSetList.removeAllElements();
- for (int i = 0; i < dataSetArray.length; i++) {
- _dataSetList.addElement(dataSetArray[i]);
- }
- } //-- void setDataSet(org.vamsas.objects.core.DataSet)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(java.lang.String modifiable)
- {
- this._modifiable = modifiable;
- } //-- void setModifiable(java.lang.String)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, org.vamsas.objects.core.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.objects.core.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(org.vamsas.objects.core.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return VAMSAS
- */
- public static org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader);
- } //-- org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader)
-
- /**
- * 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class 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
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VAMSAS target = (VAMSAS) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _modifiable
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", 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
- {
- VAMSAS target = (VAMSAS) object;
- return target.getModifiable();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.setModifiable( (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: _modifiable
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- 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( (org.vamsas.objects.core.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.objects.core.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);
- //-- _dataSetList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VAMSAS target = (VAMSAS) object;
- return target.getDataSet();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.addDataSet( (org.vamsas.objects.core.DataSet) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.DataSet();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dataSetList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.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.objects.core.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:VamsasDocument.java 264 2006-12-14 17:42:54Z JimP $
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class VamsasDocument.
- *
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
- */
-public class VamsasDocument extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Vamsas Document Version Number
- */
- private java.lang.String _version;
-
- /**
- * Field _lockFile
- */
- private org.vamsas.objects.core.LockFile _lockFile;
-
- /**
- * Field _provenance
- */
- private Provenance _provenance;
-
- /**
- * contains unassociated trees and a number of analysis sets
- *
- */
- private java.util.Vector _VAMSASList;
-
- /**
- * Field _applicationDataList
- */
- private java.util.Vector _applicationDataList;
-
- /**
- * Field _attachmentList
- */
- private java.util.Vector _attachmentList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VamsasDocument()
- {
- super();
- _VAMSASList = new Vector();
- _applicationDataList = new Vector();
- _attachmentList = new Vector();
- } //-- org.vamsas.objects.core.VamsasDocument()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addApplicationData
- *
- *
- *
- * @param vApplicationData
- */
- public void addApplicationData(ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- _applicationDataList.addElement(vApplicationData);
- } //-- void addApplicationData(ApplicationData)
-
- /**
- * Method addApplicationData
- *
- *
- *
- * @param index
- * @param vApplicationData
- */
- public void addApplicationData(int index, ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- _applicationDataList.insertElementAt(vApplicationData, index);
- } //-- void addApplicationData(int, ApplicationData)
-
- /**
- * Method addAttachment
- *
- *
- *
- * @param vAttachment
- */
- public void addAttachment(Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- _attachmentList.addElement(vAttachment);
- } //-- void addAttachment(Attachment)
-
- /**
- * Method addAttachment
- *
- *
- *
- * @param index
- * @param vAttachment
- */
- public void addAttachment(int index, Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- _attachmentList.insertElementAt(vAttachment, index);
- } //-- void addAttachment(int, Attachment)
-
- /**
- * Method addVAMSAS
- *
- *
- *
- * @param vVAMSAS
- */
- public void addVAMSAS(VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- _VAMSASList.addElement(vVAMSAS);
- } //-- void addVAMSAS(VAMSAS)
-
- /**
- * Method addVAMSAS
- *
- *
- *
- * @param index
- * @param vVAMSAS
- */
- public void addVAMSAS(int index, VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- _VAMSASList.insertElementAt(vVAMSAS, index);
- } //-- void addVAMSAS(int, VAMSAS)
-
- /**
- * Method enumerateApplicationData
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateApplicationData()
- {
- return _applicationDataList.elements();
- } //-- java.util.Enumeration enumerateApplicationData()
-
- /**
- * Method enumerateAttachment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAttachment()
- {
- return _attachmentList.elements();
- } //-- java.util.Enumeration enumerateAttachment()
-
- /**
- * Method enumerateVAMSAS
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateVAMSAS()
- {
- return _VAMSASList.elements();
- } //-- java.util.Enumeration enumerateVAMSAS()
-
- /**
- * 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 VamsasDocument) {
-
- VamsasDocument temp = (VamsasDocument)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._lockFile != null) {
- if (temp._lockFile == null) return false;
- else if (!(this._lockFile.equals(temp._lockFile)))
- return false;
- }
- else if (temp._lockFile != 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;
- if (this._VAMSASList != null) {
- if (temp._VAMSASList == null) return false;
- else if (!(this._VAMSASList.equals(temp._VAMSASList)))
- return false;
- }
- else if (temp._VAMSASList != null)
- return false;
- if (this._applicationDataList != null) {
- if (temp._applicationDataList == null) return false;
- else if (!(this._applicationDataList.equals(temp._applicationDataList)))
- return false;
- }
- else if (temp._applicationDataList != null)
- return false;
- if (this._attachmentList != null) {
- if (temp._attachmentList == null) return false;
- else if (!(this._attachmentList.equals(temp._attachmentList)))
- return false;
- }
- else if (temp._attachmentList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getApplicationData
- *
- *
- *
- * @param index
- * @return ApplicationData
- */
- public ApplicationData getApplicationData(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _applicationDataList.size())) {
- throw new IndexOutOfBoundsException("getApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
- }
-
- return (ApplicationData) _applicationDataList.elementAt(index);
- } //-- ApplicationData getApplicationData(int)
-
- /**
- * Method getApplicationData
- *
- *
- *
- * @return ApplicationData
- */
- public ApplicationData[] getApplicationData()
- {
- int size = _applicationDataList.size();
- ApplicationData[] mArray = new ApplicationData[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (ApplicationData) _applicationDataList.elementAt(index);
- }
- return mArray;
- } //-- ApplicationData[] getApplicationData()
-
- /**
- * Method getApplicationDataCount
- *
- *
- *
- * @return int
- */
- public int getApplicationDataCount()
- {
- return _applicationDataList.size();
- } //-- int getApplicationDataCount()
-
- /**
- * Method getAttachment
- *
- *
- *
- * @param index
- * @return Attachment
- */
- public Attachment getAttachment(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _attachmentList.size())) {
- throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
- }
-
- return (Attachment) _attachmentList.elementAt(index);
- } //-- Attachment getAttachment(int)
-
- /**
- * Method getAttachment
- *
- *
- *
- * @return Attachment
- */
- public Attachment[] getAttachment()
- {
- int size = _attachmentList.size();
- Attachment[] mArray = new Attachment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (Attachment) _attachmentList.elementAt(index);
- }
- return mArray;
- } //-- Attachment[] getAttachment()
-
- /**
- * Method getAttachmentCount
- *
- *
- *
- * @return int
- */
- public int getAttachmentCount()
- {
- return _attachmentList.size();
- } //-- int getAttachmentCount()
-
- /**
- * Returns the value of field 'lockFile'.
- *
- * @return LockFile
- * @return the value of field 'lockFile'.
- */
- public org.vamsas.objects.core.LockFile getLockFile()
- {
- return this._lockFile;
- } //-- org.vamsas.objects.core.LockFile getLockFile()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public Provenance getProvenance()
- {
- return this._provenance;
- } //-- Provenance getProvenance()
-
- /**
- * Method getVAMSAS
- *
- *
- *
- * @param index
- * @return VAMSAS
- */
- public VAMSAS getVAMSAS(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _VAMSASList.size())) {
- throw new IndexOutOfBoundsException("getVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
- }
-
- return (VAMSAS) _VAMSASList.elementAt(index);
- } //-- VAMSAS getVAMSAS(int)
-
- /**
- * Method getVAMSAS
- *
- *
- *
- * @return VAMSAS
- */
- public VAMSAS[] getVAMSAS()
- {
- int size = _VAMSASList.size();
- VAMSAS[] mArray = new VAMSAS[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (VAMSAS) _VAMSASList.elementAt(index);
- }
- return mArray;
- } //-- VAMSAS[] getVAMSAS()
-
- /**
- * Method getVAMSASCount
- *
- *
- *
- * @return int
- */
- public int getVAMSASCount()
- {
- return _VAMSASList.size();
- } //-- int getVAMSASCount()
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Vamsas Document Version
- * Number
- *
- * @return String
- * @return the value of field 'version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- } //-- java.lang.String 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)
-
- /**
- * Method removeAllApplicationData
- *
- */
- public void removeAllApplicationData()
- {
- _applicationDataList.removeAllElements();
- } //-- void removeAllApplicationData()
-
- /**
- * Method removeAllAttachment
- *
- */
- public void removeAllAttachment()
- {
- _attachmentList.removeAllElements();
- } //-- void removeAllAttachment()
-
- /**
- * Method removeAllVAMSAS
- *
- */
- public void removeAllVAMSAS()
- {
- _VAMSASList.removeAllElements();
- } //-- void removeAllVAMSAS()
-
- /**
- * Method removeApplicationData
- *
- *
- *
- * @param index
- * @return ApplicationData
- */
- public ApplicationData removeApplicationData(int index)
- {
- java.lang.Object obj = _applicationDataList.elementAt(index);
- _applicationDataList.removeElementAt(index);
- return (ApplicationData) obj;
- } //-- ApplicationData removeApplicationData(int)
-
- /**
- * Method removeAttachment
- *
- *
- *
- * @param index
- * @return Attachment
- */
- public Attachment removeAttachment(int index)
- {
- java.lang.Object obj = _attachmentList.elementAt(index);
- _attachmentList.removeElementAt(index);
- return (Attachment) obj;
- } //-- Attachment removeAttachment(int)
-
- /**
- * Method removeVAMSAS
- *
- *
- *
- * @param index
- * @return VAMSAS
- */
- public VAMSAS removeVAMSAS(int index)
- {
- java.lang.Object obj = _VAMSASList.elementAt(index);
- _VAMSASList.removeElementAt(index);
- return (VAMSAS) obj;
- } //-- VAMSAS removeVAMSAS(int)
-
- /**
- * Method setApplicationData
- *
- *
- *
- * @param index
- * @param vApplicationData
- */
- public void setApplicationData(int index, ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _applicationDataList.size())) {
- throw new IndexOutOfBoundsException("setApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
- }
- _applicationDataList.setElementAt(vApplicationData, index);
- } //-- void setApplicationData(int, ApplicationData)
-
- /**
- * Method setApplicationData
- *
- *
- *
- * @param applicationDataArray
- */
- public void setApplicationData(ApplicationData[] applicationDataArray)
- {
- //-- copy array
- _applicationDataList.removeAllElements();
- for (int i = 0; i < applicationDataArray.length; i++) {
- _applicationDataList.addElement(applicationDataArray[i]);
- }
- } //-- void setApplicationData(ApplicationData)
-
- /**
- * Method setAttachment
- *
- *
- *
- * @param index
- * @param vAttachment
- */
- public void setAttachment(int index, Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _attachmentList.size())) {
- throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
- }
- _attachmentList.setElementAt(vAttachment, index);
- } //-- void setAttachment(int, Attachment)
-
- /**
- * Method setAttachment
- *
- *
- *
- * @param attachmentArray
- */
- public void setAttachment(Attachment[] attachmentArray)
- {
- //-- copy array
- _attachmentList.removeAllElements();
- for (int i = 0; i < attachmentArray.length; i++) {
- _attachmentList.addElement(attachmentArray[i]);
- }
- } //-- void setAttachment(Attachment)
-
- /**
- * Sets the value of field 'lockFile'.
- *
- * @param lockFile the value of field 'lockFile'.
- */
- public void setLockFile(org.vamsas.objects.core.LockFile lockFile)
- {
- this._lockFile = lockFile;
- } //-- void setLockFile(org.vamsas.objects.core.LockFile)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(Provenance)
-
- /**
- * Method setVAMSAS
- *
- *
- *
- * @param index
- * @param vVAMSAS
- */
- public void setVAMSAS(int index, VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _VAMSASList.size())) {
- throw new IndexOutOfBoundsException("setVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
- }
- _VAMSASList.setElementAt(vVAMSAS, index);
- } //-- void setVAMSAS(int, VAMSAS)
-
- /**
- * Method setVAMSAS
- *
- *
- *
- * @param VAMSASArray
- */
- public void setVAMSAS(VAMSAS[] VAMSASArray)
- {
- //-- copy array
- _VAMSASList.removeAllElements();
- for (int i = 0; i < VAMSASArray.length; i++) {
- _VAMSASList.addElement(VAMSASArray[i]);
- }
- } //-- void setVAMSAS(VAMSAS)
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Vamsas Document Version Number
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(java.lang.String version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return VamsasDocument
- */
- public static org.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(org.vamsas.objects.core.VamsasDocument.class, reader);
- } //-- org.vamsas.objects.core.VamsasDocument 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class VamsasDocumentDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class VamsasDocumentDescriptor 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 VamsasDocumentDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.ac.uk/vamsasDocument";
- xmlName = "VamsasDocument";
-
- //-- 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
-
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.setVersion( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.ac.uk/vamsasDocument");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- 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);
- //-- _lockFile
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.LockFile.class, "_lockFile", "LockFile", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getLockFile();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.setLockFile( (org.vamsas.objects.core.LockFile) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.LockFile();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.ac.uk/vamsasDocument");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _lockFile
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(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
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.setProvenance( (Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _VAMSASList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(VAMSAS.class, "_VAMSASList", "VAMSAS", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getVAMSAS();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.addVAMSAS( (VAMSAS) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new VAMSAS();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _VAMSASList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _applicationDataList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(ApplicationData.class, "_applicationDataList", "ApplicationData", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getApplicationData();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.addApplicationData( (ApplicationData) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new ApplicationData();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _applicationDataList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _attachmentList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Attachment.class, "_attachmentList", "Attachment", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- VamsasDocument target = (VamsasDocument) object;
- return target.getAttachment();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VamsasDocument target = (VamsasDocument) object;
- target.addAttachment( (Attachment) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new Attachment();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _attachmentList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.VamsasDocumentDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return null;
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.VamsasDocument.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()
-
-}
git://source.jalview.org / vamsas.git / commitdiff