--- /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 uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Alignment()
+ {
+ super();
+ _alignmentAnnotationList = new Vector();
+ _treeList = new Vector();
+ _alignmentSequenceList = new Vector();
+ _propertyList = new Vector();
+ } //-- uk.ac.vamsas.objects.core.Alignment()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignmentAnnotation
+ *
+ *
+ *
+ * @param vAlignmentAnnotation
+ */
+ public void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentAnnotationList.addElement(vAlignmentAnnotation);
+ } //-- void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation)
+
+ /**
+ * Method addAlignmentAnnotation
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentAnnotation
+ */
+ public void addAlignmentAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
+ } //-- void addAlignmentAnnotation(int, uk.ac.vamsas.objects.core.AlignmentAnnotation)
+
+ /**
+ * Method addAlignmentSequence
+ *
+ *
+ *
+ * @param vAlignmentSequence
+ */
+ public void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceList.addElement(vAlignmentSequence);
+ } //-- void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method addAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ */
+ public void addAlignmentSequence(int index, uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
+ } //-- void addAlignmentSequence(int, uk.ac.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param vTree
+ */
+ public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.addElement(vTree);
+ } //-- void addTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
+
+ /**
+ * Method getAlignmentAnnotation
+ *
+ *
+ *
+ * @return AlignmentAnnotation
+ */
+ public uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ int size = _alignmentAnnotationList.size();
+ uk.ac.vamsas.objects.core.AlignmentAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentAnnotation[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
+
+ /**
+ * Method getAlignmentAnnotationCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentAnnotationCount()
+ {
+ return _alignmentAnnotationList.size();
+ } //-- int getAlignmentAnnotationCount()
+
+ /**
+ * Method getAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequence
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
+
+ /**
+ * Method getAlignmentSequence
+ *
+ *
+ *
+ * @return AlignmentSequence
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
+ {
+ int size = _alignmentSequenceList.size();
+ uk.ac.vamsas.objects.core.AlignmentSequence[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequence[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree[] getTree()
+ {
+ int size = _treeList.size();
+ uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
+ {
+ java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
+ _alignmentAnnotationList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.AlignmentAnnotation) obj;
+ } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
+
+ /**
+ * Method removeAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequence
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
+ {
+ java.lang.Object obj = _alignmentSequenceList.elementAt(index);
+ _alignmentSequenceList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.AlignmentSequence) obj;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Method removeTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTree(int index)
+ {
+ java.lang.Object obj = _treeList.elementAt(index);
+ _treeList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.AlignmentAnnotation)
+
+ /**
+ * Method setAlignmentAnnotation
+ *
+ *
+ *
+ * @param alignmentAnnotationArray
+ */
+ public void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
+ {
+ //-- copy array
+ _alignmentAnnotationList.removeAllElements();
+ for (int i = 0; i < alignmentAnnotationArray.length; i++) {
+ _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
+ }
+ } //-- void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation)
+
+ /**
+ * Method setAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ */
+ public void setAlignmentSequence(int index, uk.ac.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, uk.ac.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method setAlignmentSequence
+ *
+ *
+ *
+ * @param alignmentSequenceArray
+ */
+ public void setAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
+ {
+ //-- copy array
+ _alignmentSequenceList.removeAllElements();
+ for (int i = 0; i < alignmentSequenceArray.length; i++) {
+ _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
+ }
+ } //-- void setAlignmentSequence(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void setTree(int index, uk.ac.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, uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param treeArray
+ */
+ public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
+ {
+ //-- copy array
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
+ }
+ } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Alignment
+ */
+ public static uk.ac.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Alignment.class, reader);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlignmentAnnotation() \r
+ {\r
+ super();\r
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()\r
+ {\r
+ return this._provenance;\r
+ } //-- uk.ac.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(uk.ac.vamsas.objects.core.Provenance provenance)\r
+ {\r
+ this._provenance = provenance;\r
+ } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return RangeType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentAnnotation.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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:AlignmentDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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:AlignmentSequence.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class AlignmentSequence extends uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.AlignmentSequence()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param vAlignmentSequenceAnnotation
+ */
+ public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
+ } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Method addAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequenceAnnotation
+ */
+ public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
+ } //-- void addAlignmentSequenceAnnotation(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
+
+ /**
+ * Method getAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @return AlignmentSequenceAnnotation
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
+ {
+ int size = _alignmentSequenceAnnotationList.size();
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
+ {
+ java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
+ _alignmentSequenceAnnotationList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Method setAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param alignmentSequenceAnnotationArray
+ */
+ public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
+ {
+ //-- copy array
+ _alignmentSequenceAnnotationList.removeAllElements();
+ for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
+ _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+ }
+ } //-- void setAlignmentSequenceAnnotation(uk.ac.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 uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlignmentSequenceAnnotation() \r
+ {\r
+ super();\r
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()\r
+ {\r
+ return this._provenance;\r
+ } //-- uk.ac.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(uk.ac.vamsas.objects.core.Provenance provenance)\r
+ {\r
+ this._provenance = provenance;\r
+ } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return RangeType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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:AlignmentSequenceDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class AlignmentSequenceDescriptor extends uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.AnnotationElement()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addGlyph
+ *
+ *
+ *
+ * @param vGlyph
+ */
+ public void addGlyph(uk.ac.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _glyphList.addElement(vGlyph);
+ } //-- void addGlyph(uk.ac.vamsas.objects.core.Glyph)
+
+ /**
+ * Method addGlyph
+ *
+ *
+ *
+ * @param index
+ * @param vGlyph
+ */
+ public void addGlyph(int index, uk.ac.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _glyphList.insertElementAt(vGlyph, index);
+ } //-- void addGlyph(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Glyph getGlyph(int)
+
+ /**
+ * Method getGlyph
+ *
+ *
+ *
+ * @return Glyph
+ */
+ public uk.ac.vamsas.objects.core.Glyph[] getGlyph()
+ {
+ int size = _glyphList.size();
+ uk.ac.vamsas.objects.core.Glyph[] mArray = new uk.ac.vamsas.objects.core.Glyph[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Glyph removeGlyph(int index)
+ {
+ java.lang.Object obj = _glyphList.elementAt(index);
+ _glyphList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Glyph) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Glyph)
+
+ /**
+ * Method setGlyph
+ *
+ *
+ *
+ * @param glyphArray
+ */
+ public void setGlyph(uk.ac.vamsas.objects.core.Glyph[] glyphArray)
+ {
+ //-- copy array
+ _glyphList.removeAllElements();
+ for (int i = 0; i < glyphArray.length; i++) {
+ _glyphList.addElement(glyphArray[i]);
+ }
+ } //-- void setGlyph(uk.ac.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 uk.ac.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AnnotationElement.class, reader);
+ } //-- uk.ac.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:AnnotationElementDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AppData.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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:ApplicationData.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class ApplicationData extends uk.ac.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 uk.ac.vamsas.objects.core.Common _common;
+
+ /**
+ * Field _instanceList
+ */
+ private java.util.Vector _instanceList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public ApplicationData()
+ {
+ super();
+ _userList = new Vector();
+ _instanceList = new Vector();
+ } //-- uk.ac.vamsas.objects.core.ApplicationData()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addInstance
+ *
+ *
+ *
+ * @param vInstance
+ */
+ public void addInstance(uk.ac.vamsas.objects.core.Instance vInstance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _instanceList.addElement(vInstance);
+ } //-- void addInstance(uk.ac.vamsas.objects.core.Instance)
+
+ /**
+ * Method addInstance
+ *
+ *
+ *
+ * @param index
+ * @param vInstance
+ */
+ public void addInstance(int index, uk.ac.vamsas.objects.core.Instance vInstance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _instanceList.insertElementAt(vInstance, index);
+ } //-- void addInstance(int, uk.ac.vamsas.objects.core.Instance)
+
+ /**
+ * Method addUser
+ *
+ *
+ *
+ * @param vUser
+ */
+ public void addUser(uk.ac.vamsas.objects.core.User vUser)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _userList.addElement(vUser);
+ } //-- void addUser(uk.ac.vamsas.objects.core.User)
+
+ /**
+ * Method addUser
+ *
+ *
+ *
+ * @param index
+ * @param vUser
+ */
+ public void addUser(int index, uk.ac.vamsas.objects.core.User vUser)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _userList.insertElementAt(vUser, index);
+ } //-- void addUser(int, uk.ac.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 uk.ac.vamsas.objects.core.Common getCommon()
+ {
+ return this._common;
+ } //-- uk.ac.vamsas.objects.core.Common getCommon()
+
+ /**
+ * Method getInstance
+ *
+ *
+ *
+ * @param index
+ * @return Instance
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Instance) _instanceList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Instance getInstance(int)
+
+ /**
+ * Method getInstance
+ *
+ *
+ *
+ * @return Instance
+ */
+ public uk.ac.vamsas.objects.core.Instance[] getInstance()
+ {
+ int size = _instanceList.size();
+ uk.ac.vamsas.objects.core.Instance[] mArray = new uk.ac.vamsas.objects.core.Instance[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Instance) _instanceList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.User) _userList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.User getUser(int)
+
+ /**
+ * Method getUser
+ *
+ *
+ *
+ * @return User
+ */
+ public uk.ac.vamsas.objects.core.User[] getUser()
+ {
+ int size = _userList.size();
+ uk.ac.vamsas.objects.core.User[] mArray = new uk.ac.vamsas.objects.core.User[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.User) _userList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Instance removeInstance(int index)
+ {
+ java.lang.Object obj = _instanceList.elementAt(index);
+ _instanceList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Instance) obj;
+ } //-- uk.ac.vamsas.objects.core.Instance removeInstance(int)
+
+ /**
+ * Method removeUser
+ *
+ *
+ *
+ * @param index
+ * @return User
+ */
+ public uk.ac.vamsas.objects.core.User removeUser(int index)
+ {
+ java.lang.Object obj = _userList.elementAt(index);
+ _userList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.User) obj;
+ } //-- uk.ac.vamsas.objects.core.User removeUser(int)
+
+ /**
+ * Sets the value of field 'common'.
+ *
+ * @param common the value of field 'common'.
+ */
+ public void setCommon(uk.ac.vamsas.objects.core.Common common)
+ {
+ this._common = common;
+ } //-- void setCommon(uk.ac.vamsas.objects.core.Common)
+
+ /**
+ * Method setInstance
+ *
+ *
+ *
+ * @param index
+ * @param vInstance
+ */
+ public void setInstance(int index, uk.ac.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, uk.ac.vamsas.objects.core.Instance)
+
+ /**
+ * Method setInstance
+ *
+ *
+ *
+ * @param instanceArray
+ */
+ public void setInstance(uk.ac.vamsas.objects.core.Instance[] instanceArray)
+ {
+ //-- copy array
+ _instanceList.removeAllElements();
+ for (int i = 0; i < instanceArray.length; i++) {
+ _instanceList.addElement(instanceArray[i]);
+ }
+ } //-- void setInstance(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.User)
+
+ /**
+ * Method setUser
+ *
+ *
+ *
+ * @param userArray
+ */
+ public void setUser(uk.ac.vamsas.objects.core.User[] userArray)
+ {
+ //-- copy array
+ _userList.removeAllElements();
+ for (int i = 0; i < userArray.length; i++) {
+ _userList.addElement(userArray[i]);
+ }
+ } //-- void setUser(uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.ApplicationData.class, reader);
+ } //-- uk.ac.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:ApplicationDataDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class ApplicationDataDescriptor extends uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Attachment.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.AppData \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Common() \r
+ {\r
+ super();\r
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Common) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Common.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.AppDataDescriptor());\r
+ nsURI = "http://www.vamsas.org";\r
+ xmlName = "Common";\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public DataSet()
+ {
+ super();
+ _sequenceList = new Vector();
+ _dataSetAnnotationsList = new Vector();
+ _alignmentList = new Vector();
+ _treeList = new Vector();
+ } //-- uk.ac.vamsas.objects.core.DataSet()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param vAlignment
+ */
+ public void addAlignment(uk.ac.vamsas.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.addElement(vAlignment);
+ } //-- void addAlignment(uk.ac.vamsas.objects.core.Alignment)
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param index
+ * @param vAlignment
+ */
+ public void addAlignment(int index, uk.ac.vamsas.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.insertElementAt(vAlignment, index);
+ } //-- void addAlignment(int, uk.ac.vamsas.objects.core.Alignment)
+
+ /**
+ * Method addDataSetAnnotations
+ *
+ *
+ *
+ * @param vDataSetAnnotations
+ */
+ public void addDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetAnnotationsList.addElement(vDataSetAnnotations);
+ } //-- void addDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations)
+
+ /**
+ * Method addDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vDataSetAnnotations
+ */
+ public void addDataSetAnnotations(int index, uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index);
+ } //-- void addDataSetAnnotations(int, uk.ac.vamsas.objects.core.DataSetAnnotations)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param vSequence
+ */
+ public void addSequence(uk.ac.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.addElement(vSequence);
+ } //-- void addSequence(uk.ac.vamsas.objects.core.Sequence)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void addSequence(int index, uk.ac.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.insertElementAt(vSequence, index);
+ } //-- void addSequence(int, uk.ac.vamsas.objects.core.Sequence)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param vTree
+ */
+ public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.addElement(vTree);
+ } //-- void addTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Alignment getAlignment(int)
+
+ /**
+ * Method getAlignment
+ *
+ *
+ *
+ * @return Alignment
+ */
+ public uk.ac.vamsas.objects.core.Alignment[] getAlignment()
+ {
+ int size = _alignmentList.size();
+ uk.ac.vamsas.objects.core.Alignment[] mArray = new uk.ac.vamsas.objects.core.Alignment[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Alignment[] getAlignment()
+
+ /**
+ * Method getAlignmentCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentCount()
+ {
+ return _alignmentList.size();
+ } //-- int getAlignmentCount()
+
+ /**
+ * Method getDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return DataSetAnnotations
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int)
+
+ /**
+ * Method getDataSetAnnotations
+ *
+ *
+ *
+ * @return DataSetAnnotations
+ */
+ public uk.ac.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
+ {
+ int size = _dataSetAnnotationsList.size();
+ uk.ac.vamsas.objects.core.DataSetAnnotations[] mArray = new uk.ac.vamsas.objects.core.DataSetAnnotations[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @param index
+ * @return Sequence
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Sequence getSequence(int)
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @return Sequence
+ */
+ public uk.ac.vamsas.objects.core.Sequence[] getSequence()
+ {
+ int size = _sequenceList.size();
+ uk.ac.vamsas.objects.core.Sequence[] mArray = new uk.ac.vamsas.objects.core.Sequence[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Sequence[] getSequence()
+
+ /**
+ * Method getSequenceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSequenceCount()
+ {
+ return _sequenceList.size();
+ } //-- int getSequenceCount()
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree[] getTree()
+ {
+ int size = _treeList.size();
+ uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Alignment removeAlignment(int index)
+ {
+ java.lang.Object obj = _alignmentList.elementAt(index);
+ _alignmentList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Alignment) obj;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
+ {
+ java.lang.Object obj = _dataSetAnnotationsList.elementAt(index);
+ _dataSetAnnotationsList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj;
+ } //-- uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int)
+
+ /**
+ * Method removeSequence
+ *
+ *
+ *
+ * @param index
+ * @return Sequence
+ */
+ public uk.ac.vamsas.objects.core.Sequence removeSequence(int index)
+ {
+ java.lang.Object obj = _sequenceList.elementAt(index);
+ _sequenceList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Sequence) obj;
+ } //-- uk.ac.vamsas.objects.core.Sequence removeSequence(int)
+
+ /**
+ * Method removeTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTree(int index)
+ {
+ java.lang.Object obj = _treeList.elementAt(index);
+ _treeList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ } //-- uk.ac.vamsas.objects.core.Tree removeTree(int)
+
+ /**
+ * Method setAlignment
+ *
+ *
+ *
+ * @param index
+ * @param vAlignment
+ */
+ public void setAlignment(int index, uk.ac.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, uk.ac.vamsas.objects.core.Alignment)
+
+ /**
+ * Method setAlignment
+ *
+ *
+ *
+ * @param alignmentArray
+ */
+ public void setAlignment(uk.ac.vamsas.objects.core.Alignment[] alignmentArray)
+ {
+ //-- copy array
+ _alignmentList.removeAllElements();
+ for (int i = 0; i < alignmentArray.length; i++) {
+ _alignmentList.addElement(alignmentArray[i]);
+ }
+ } //-- void setAlignment(uk.ac.vamsas.objects.core.Alignment)
+
+ /**
+ * Method setDataSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vDataSetAnnotations
+ */
+ public void setDataSetAnnotations(int index, uk.ac.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, uk.ac.vamsas.objects.core.DataSetAnnotations)
+
+ /**
+ * Method setDataSetAnnotations
+ *
+ *
+ *
+ * @param dataSetAnnotationsArray
+ */
+ public void setDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray)
+ {
+ //-- copy array
+ _dataSetAnnotationsList.removeAllElements();
+ for (int i = 0; i < dataSetAnnotationsArray.length; i++) {
+ _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]);
+ }
+ } //-- void setDataSetAnnotations(uk.ac.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(uk.ac.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void setSequence(int index, uk.ac.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, uk.ac.vamsas.objects.core.Sequence)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param sequenceArray
+ */
+ public void setSequence(uk.ac.vamsas.objects.core.Sequence[] sequenceArray)
+ {
+ //-- copy array
+ _sequenceList.removeAllElements();
+ for (int i = 0; i < sequenceArray.length; i++) {
+ _sequenceList.addElement(sequenceArray[i]);
+ }
+ } //-- void setSequence(uk.ac.vamsas.objects.core.Sequence)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void setTree(int index, uk.ac.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, uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param treeArray
+ */
+ public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
+ {
+ //-- copy array
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
+ }
+ } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return DataSet
+ */
+ public static uk.ac.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSet.class, reader);
+ } //-- uk.ac.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:DataSetAnnotations.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class DataSetAnnotations extends uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public DataSetAnnotations()
+ {
+ super();
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- uk.ac.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(uk.ac.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(uk.ac.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 uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader);
+ } //-- uk.ac.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:DataSetAnnotationsDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class DataSetAnnotationsDescriptor extends uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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:DataSetDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.DbRef()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addLink
+ *
+ *
+ *
+ * @param vLink
+ */
+ public void addLink(uk.ac.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.addElement(vLink);
+ } //-- void addLink(uk.ac.vamsas.objects.core.Link)
+
+ /**
+ * Method addLink
+ *
+ *
+ *
+ * @param index
+ * @param vLink
+ */
+ public void addLink(int index, uk.ac.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.insertElementAt(vLink, index);
+ } //-- void addLink(int, uk.ac.vamsas.objects.core.Link)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param vMap
+ */
+ public void addMap(uk.ac.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.addElement(vMap);
+ } //-- void addMap(uk.ac.vamsas.objects.core.Map)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void addMap(int index, uk.ac.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.insertElementAt(vMap, index);
+ } //-- void addMap(int, uk.ac.vamsas.objects.core.Map)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Link getLink(int)
+
+ /**
+ * Method getLink
+ *
+ *
+ *
+ * @return Link
+ */
+ public uk.ac.vamsas.objects.core.Link[] getLink()
+ {
+ int size = _linkList.size();
+ uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Link[] getLink()
+
+ /**
+ * Method getLinkCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getLinkCount()
+ {
+ return _linkList.size();
+ } //-- int getLinkCount()
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Map getMap(int)
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @return Map
+ */
+ public uk.ac.vamsas.objects.core.Map[] getMap()
+ {
+ int size = _mapList.size();
+ uk.ac.vamsas.objects.core.Map[] mArray = new uk.ac.vamsas.objects.core.Map[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Map[] getMap()
+
+ /**
+ * Method getMapCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getMapCount()
+ {
+ return _mapList.size();
+ } //-- int getMapCount()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Link removeLink(int index)
+ {
+ java.lang.Object obj = _linkList.elementAt(index);
+ _linkList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Link) obj;
+ } //-- uk.ac.vamsas.objects.core.Link removeLink(int)
+
+ /**
+ * Method removeMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public uk.ac.vamsas.objects.core.Map removeMap(int index)
+ {
+ java.lang.Object obj = _mapList.elementAt(index);
+ _mapList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Map) obj;
+ } //-- uk.ac.vamsas.objects.core.Map removeMap(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Link)
+
+ /**
+ * Method setLink
+ *
+ *
+ *
+ * @param linkArray
+ */
+ public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray)
+ {
+ //-- copy array
+ _linkList.removeAllElements();
+ for (int i = 0; i < linkArray.length; i++) {
+ _linkList.addElement(linkArray[i]);
+ }
+ } //-- void setLink(uk.ac.vamsas.objects.core.Link)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void setMap(int index, uk.ac.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, uk.ac.vamsas.objects.core.Map)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param mapArray
+ */
+ public void setMap(uk.ac.vamsas.objects.core.Map[] mapArray)
+ {
+ //-- copy array
+ _mapList.removeAllElements();
+ for (int i = 0; i < mapArray.length; i++) {
+ _mapList.addElement(mapArray[i]);
+ }
+ } //-- void setMap(uk.ac.vamsas.objects.core.Map)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, uk.ac.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, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(uk.ac.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 uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DbRef.class, reader);
+ } //-- uk.ac.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:DbRefDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.Entry()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addInput
+ *
+ *
+ *
+ * @param vInput
+ */
+ public void addInput(uk.ac.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _inputList.addElement(vInput);
+ } //-- void addInput(uk.ac.vamsas.objects.core.Input)
+
+ /**
+ * Method addInput
+ *
+ *
+ *
+ * @param index
+ * @param vInput
+ */
+ public void addInput(int index, uk.ac.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _inputList.insertElementAt(vInput, index);
+ } //-- void addInput(int, uk.ac.vamsas.objects.core.Input)
+
+ /**
+ * Method addParam
+ *
+ *
+ *
+ * @param vParam
+ */
+ public void addParam(uk.ac.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _paramList.addElement(vParam);
+ } //-- void addParam(uk.ac.vamsas.objects.core.Param)
+
+ /**
+ * Method addParam
+ *
+ *
+ *
+ * @param index
+ * @param vParam
+ */
+ public void addParam(int index, uk.ac.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _paramList.insertElementAt(vParam, index);
+ } //-- void addParam(int, uk.ac.vamsas.objects.core.Param)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Input getInput(int)
+
+ /**
+ * Method getInput
+ *
+ *
+ *
+ * @return Input
+ */
+ public uk.ac.vamsas.objects.core.Input[] getInput()
+ {
+ int size = _inputList.size();
+ uk.ac.vamsas.objects.core.Input[] mArray = new uk.ac.vamsas.objects.core.Input[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Input[] getInput()
+
+ /**
+ * Method getInputCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getInputCount()
+ {
+ return _inputList.size();
+ } //-- int getInputCount()
+
+ /**
+ * Method getParam
+ *
+ *
+ *
+ * @param index
+ * @return Param
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Param getParam(int)
+
+ /**
+ * Method getParam
+ *
+ *
+ *
+ * @return Param
+ */
+ public uk.ac.vamsas.objects.core.Param[] getParam()
+ {
+ int size = _paramList.size();
+ uk.ac.vamsas.objects.core.Param[] mArray = new uk.ac.vamsas.objects.core.Param[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Param[] getParam()
+
+ /**
+ * Method getParamCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getParamCount()
+ {
+ return _paramList.size();
+ } //-- int getParamCount()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Input removeInput(int index)
+ {
+ java.lang.Object obj = _inputList.elementAt(index);
+ _inputList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Input) obj;
+ } //-- uk.ac.vamsas.objects.core.Input removeInput(int)
+
+ /**
+ * Method removeParam
+ *
+ *
+ *
+ * @param index
+ * @return Param
+ */
+ public uk.ac.vamsas.objects.core.Param removeParam(int index)
+ {
+ java.lang.Object obj = _paramList.elementAt(index);
+ _paramList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Param) obj;
+ } //-- uk.ac.vamsas.objects.core.Param removeParam(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Input)
+
+ /**
+ * Method setInput
+ *
+ *
+ *
+ * @param inputArray
+ */
+ public void setInput(uk.ac.vamsas.objects.core.Input[] inputArray)
+ {
+ //-- copy array
+ _inputList.removeAllElements();
+ for (int i = 0; i < inputArray.length; i++) {
+ _inputList.addElement(inputArray[i]);
+ }
+ } //-- void setInput(uk.ac.vamsas.objects.core.Input)
+
+ /**
+ * Method setParam
+ *
+ *
+ *
+ * @param index
+ * @param vParam
+ */
+ public void setParam(int index, uk.ac.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, uk.ac.vamsas.objects.core.Param)
+
+ /**
+ * Method setParam
+ *
+ *
+ *
+ * @param paramArray
+ */
+ public void setParam(uk.ac.vamsas.objects.core.Param[] paramArray)
+ {
+ //-- copy array
+ _paramList.removeAllElements();
+ for (int i = 0; i < paramArray.length; i++) {
+ _paramList.addElement(paramArray[i]);
+ }
+ } //-- void setParam(uk.ac.vamsas.objects.core.Param)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, uk.ac.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, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(uk.ac.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 uk.ac.vamsas.objects.core.Entry unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Entry.class, reader);
+ } //-- uk.ac.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:EntryDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Glyph.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Input) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Input.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Instance) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Instance.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Link unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Link) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Link.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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("");
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.LockFile unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.LockFile) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.LockFile.class, reader);
+ } //-- uk.ac.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:LockFileDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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
+
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.MapList \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Map() \r
+ {\r
+ super();\r
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Map) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Map.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.MapListDescriptor());\r
+ nsURI = "http://www.vamsas.org";\r
+ xmlName = "map";\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.MapList) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.MapList.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Mapping) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Mapping.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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("");
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Newick unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Newick) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Newick.class, reader);
+ } //-- uk.ac.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:NewickDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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
+
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Param unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Param) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Param.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Pos unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Pos) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Pos.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Property unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Property) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Property.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.Provenance()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addEntry
+ *
+ *
+ *
+ * @param vEntry
+ */
+ public void addEntry(uk.ac.vamsas.objects.core.Entry vEntry)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _entryList.addElement(vEntry);
+ } //-- void addEntry(uk.ac.vamsas.objects.core.Entry)
+
+ /**
+ * Method addEntry
+ *
+ *
+ *
+ * @param index
+ * @param vEntry
+ */
+ public void addEntry(int index, uk.ac.vamsas.objects.core.Entry vEntry)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _entryList.insertElementAt(vEntry, index);
+ } //-- void addEntry(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Entry) _entryList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Entry getEntry(int)
+
+ /**
+ * Method getEntry
+ *
+ *
+ *
+ * @return Entry
+ */
+ public uk.ac.vamsas.objects.core.Entry[] getEntry()
+ {
+ int size = _entryList.size();
+ uk.ac.vamsas.objects.core.Entry[] mArray = new uk.ac.vamsas.objects.core.Entry[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Entry) _entryList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Entry removeEntry(int index)
+ {
+ java.lang.Object obj = _entryList.elementAt(index);
+ _entryList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Entry) obj;
+ } //-- uk.ac.vamsas.objects.core.Entry removeEntry(int)
+
+ /**
+ * Method setEntry
+ *
+ *
+ *
+ * @param index
+ * @param vEntry
+ */
+ public void setEntry(int index, uk.ac.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, uk.ac.vamsas.objects.core.Entry)
+
+ /**
+ * Method setEntry
+ *
+ *
+ *
+ * @param entryArray
+ */
+ public void setEntry(uk.ac.vamsas.objects.core.Entry[] entryArray)
+ {
+ //-- copy array
+ _entryList.removeAllElements();
+ for (int i = 0; i < entryArray.length; i++) {
+ _entryList.addElement(entryArray[i]);
+ }
+ } //-- void setEntry(uk.ac.vamsas.objects.core.Entry)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Provenance
+ */
+ public static uk.ac.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Provenance.class, reader);
+ } //-- uk.ac.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:ProvenanceDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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(uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.addElement(vAnnotationElement);\r
+ } //-- void addAnnotationElement(uk.ac.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, uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.insertElementAt(vAnnotationElement, index);\r
+ } //-- void addAnnotationElement(int, uk.ac.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Method addLink\r
+ * \r
+ * \r
+ * \r
+ * @param vLink\r
+ */\r
+ public void addLink(uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _linkList.addElement(vLink);\r
+ } //-- void addLink(uk.ac.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, uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _linkList.insertElementAt(vLink, index);\r
+ } //-- void addLink(int, uk.ac.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Method addProperty\r
+ * \r
+ * \r
+ * \r
+ * @param vProperty\r
+ */\r
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.addElement(vProperty);\r
+ } //-- void addProperty(uk.ac.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, uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.insertElementAt(vProperty, index);\r
+ } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method addScore\r
+ * \r
+ * \r
+ * \r
+ * @param vScore\r
+ */\r
+ public void addScore(uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _scoreList.addElement(vScore);\r
+ } //-- void addScore(uk.ac.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, uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _scoreList.insertElementAt(vScore, index);\r
+ } //-- void addScore(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
+ } //-- uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(int) \r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @return AnnotationElement\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement()\r
+ {\r
+ int size = _annotationElementList.size();\r
+ uk.ac.vamsas.objects.core.AnnotationElement[] mArray = new uk.ac.vamsas.objects.core.AnnotationElement[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);\r
+ } //-- uk.ac.vamsas.objects.core.Link getLink(int) \r
+\r
+ /**\r
+ * Method getLink\r
+ * \r
+ * \r
+ * \r
+ * @return Link\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link[] getLink()\r
+ {\r
+ int size = _linkList.size();\r
+ uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int) \r
+\r
+ /**\r
+ * Method getProperty\r
+ * \r
+ * \r
+ * \r
+ * @return Property\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property[] getProperty()\r
+ {\r
+ int size = _propertyList.size();\r
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
+ } //-- uk.ac.vamsas.objects.core.Score getScore(int) \r
+\r
+ /**\r
+ * Method getScore\r
+ * \r
+ * \r
+ * \r
+ * @return Score\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score[] getScore()\r
+ {\r
+ int size = _scoreList.size();\r
+ uk.ac.vamsas.objects.core.Score[] mArray = new uk.ac.vamsas.objects.core.Score[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)\r
+ {\r
+ java.lang.Object obj = _annotationElementList.elementAt(index);\r
+ _annotationElementList.removeElementAt(index);\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) obj;\r
+ } //-- uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) \r
+\r
+ /**\r
+ * Method removeLink\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Link\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link removeLink(int index)\r
+ {\r
+ java.lang.Object obj = _linkList.elementAt(index);\r
+ _linkList.removeElementAt(index);\r
+ return (uk.ac.vamsas.objects.core.Link) obj;\r
+ } //-- uk.ac.vamsas.objects.core.Link removeLink(int) \r
+\r
+ /**\r
+ * Method removeProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Property\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property removeProperty(int index)\r
+ {\r
+ java.lang.Object obj = _propertyList.elementAt(index);\r
+ _propertyList.removeElementAt(index);\r
+ return (uk.ac.vamsas.objects.core.Property) obj;\r
+ } //-- uk.ac.vamsas.objects.core.Property removeProperty(int) \r
+\r
+ /**\r
+ * Method removeScore\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Score\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score removeScore(int index)\r
+ {\r
+ java.lang.Object obj = _scoreList.elementAt(index);\r
+ _scoreList.removeElementAt(index);\r
+ return (uk.ac.vamsas.objects.core.Score) obj;\r
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.AnnotationElement) \r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param annotationElementArray\r
+ */\r
+ public void setAnnotationElement(uk.ac.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(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Link) \r
+\r
+ /**\r
+ * Method setLink\r
+ * \r
+ * \r
+ * \r
+ * @param linkArray\r
+ */\r
+ public void setLink(uk.ac.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(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Property) \r
+\r
+ /**\r
+ * Method setProperty\r
+ * \r
+ * \r
+ * \r
+ * @param propertyArray\r
+ */\r
+ public void setProperty(uk.ac.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(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Score) \r
+\r
+ /**\r
+ * Method setScore\r
+ * \r
+ * \r
+ * \r
+ * @param scoreArray\r
+ */\r
+ public void setScore(uk.ac.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(uk.ac.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 uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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(uk.ac.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( (uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Score unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Score) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Score.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Seg unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (uk.ac.vamsas.objects.core.Seg) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Seg.class, reader);\r
+ } //-- uk.ac.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 uk.ac.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
+ } //-- uk.ac.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 uk.ac.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:Sequence.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class Sequence extends uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.Sequence()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param vDbRef
+ */
+ public void addDbRef(uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.addElement(vDbRef);
+ } //-- void addDbRef(uk.ac.vamsas.objects.core.DbRef)
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void addDbRef(int index, uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.insertElementAt(vDbRef, index);
+ } //-- void addDbRef(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.DbRef getDbRef(int)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @return DbRef
+ */
+ public uk.ac.vamsas.objects.core.DbRef[] getDbRef()
+ {
+ int size = _dbRefList.size();
+ uk.ac.vamsas.objects.core.DbRef[] mArray = new uk.ac.vamsas.objects.core.DbRef[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.DbRef removeDbRef(int index)
+ {
+ java.lang.Object obj = _dbRefList.elementAt(index);
+ _dbRefList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.DbRef) obj;
+ } //-- uk.ac.vamsas.objects.core.DbRef removeDbRef(int)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void setDbRef(int index, uk.ac.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, uk.ac.vamsas.objects.core.DbRef)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param dbRefArray
+ */
+ public void setDbRef(uk.ac.vamsas.objects.core.DbRef[] dbRefArray)
+ {
+ //-- copy array
+ _dbRefList.removeAllElements();
+ for (int i = 0; i < dbRefArray.length; i++) {
+ _dbRefList.addElement(dbRefArray[i]);
+ }
+ } //-- void setDbRef(uk.ac.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 uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.class, reader);
+ } //-- uk.ac.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:SequenceDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class SequenceDescriptor extends uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.SequenceType()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addMapping
+ *
+ *
+ *
+ * @param vMapping
+ */
+ public void addMapping(uk.ac.vamsas.objects.core.Mapping vMapping)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mappingList.addElement(vMapping);
+ } //-- void addMapping(uk.ac.vamsas.objects.core.Mapping)
+
+ /**
+ * Method addMapping
+ *
+ *
+ *
+ * @param index
+ * @param vMapping
+ */
+ public void addMapping(int index, uk.ac.vamsas.objects.core.Mapping vMapping)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mappingList.insertElementAt(vMapping, index);
+ } //-- void addMapping(int, uk.ac.vamsas.objects.core.Mapping)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Mapping getMapping(int)
+
+ /**
+ * Method getMapping
+ *
+ *
+ *
+ * @return Mapping
+ */
+ public uk.ac.vamsas.objects.core.Mapping[] getMapping()
+ {
+ int size = _mappingList.size();
+ uk.ac.vamsas.objects.core.Mapping[] mArray = new uk.ac.vamsas.objects.core.Mapping[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Mapping removeMapping(int index)
+ {
+ java.lang.Object obj = _mappingList.elementAt(index);
+ _mappingList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Mapping) obj;
+ } //-- uk.ac.vamsas.objects.core.Mapping removeMapping(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Mapping)
+
+ /**
+ * Method setMapping
+ *
+ *
+ *
+ * @param mappingArray
+ */
+ public void setMapping(uk.ac.vamsas.objects.core.Mapping[] mappingArray)
+ {
+ //-- copy array
+ _mappingList.removeAllElements();
+ for (int i = 0; i < mappingArray.length; i++) {
+ _mappingList.addElement(mappingArray[i]);
+ }
+ } //-- void setMapping(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(uk.ac.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 uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.SequenceType.class, reader);
+ } //-- uk.ac.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:SequenceTypeDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree()
+ {
+ super();
+ _newickList = new Vector();
+ _propertyList = new Vector();
+ } //-- uk.ac.vamsas.objects.core.Tree()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addNewick
+ *
+ *
+ *
+ * @param vNewick
+ */
+ public void addNewick(uk.ac.vamsas.objects.core.Newick vNewick)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _newickList.addElement(vNewick);
+ } //-- void addNewick(uk.ac.vamsas.objects.core.Newick)
+
+ /**
+ * Method addNewick
+ *
+ *
+ *
+ * @param index
+ * @param vNewick
+ */
+ public void addNewick(int index, uk.ac.vamsas.objects.core.Newick vNewick)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _newickList.insertElementAt(vNewick, index);
+ } //-- void addNewick(int, uk.ac.vamsas.objects.core.Newick)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Newick) _newickList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Newick getNewick(int)
+
+ /**
+ * Method getNewick
+ *
+ *
+ *
+ * @return Newick
+ */
+ public uk.ac.vamsas.objects.core.Newick[] getNewick()
+ {
+ int size = _newickList.size();
+ uk.ac.vamsas.objects.core.Newick[] mArray = new uk.ac.vamsas.objects.core.Newick[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Newick) _newickList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.vamsas.objects.core.Newick[] getNewick()
+
+ /**
+ * Method getNewickCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getNewickCount()
+ {
+ return _newickList.size();
+ } //-- int getNewickCount()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.Newick removeNewick(int index)
+ {
+ java.lang.Object obj = _newickList.elementAt(index);
+ _newickList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Newick) obj;
+ } //-- uk.ac.vamsas.objects.core.Newick removeNewick(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public uk.ac.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Newick)
+
+ /**
+ * Method setNewick
+ *
+ *
+ *
+ * @param newickArray
+ */
+ public void setNewick(uk.ac.vamsas.objects.core.Newick[] newickArray)
+ {
+ //-- copy array
+ _newickList.removeAllElements();
+ for (int i = 0; i < newickArray.length; i++) {
+ _newickList.addElement(newickArray[i]);
+ }
+ } //-- void setNewick(uk.ac.vamsas.objects.core.Newick)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, uk.ac.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, uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(uk.ac.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 uk.ac.vamsas.objects.core.Tree unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.Tree) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Tree.class, reader);
+ } //-- uk.ac.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:TreeDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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:User.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class User extends uk.ac.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();
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.User) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.User.class, reader);
+ } //-- uk.ac.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:UserDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+public class UserDescriptor extends uk.ac.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 uk.ac.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
+
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.vamsas.objects.core.VAMSAS()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addDataSet
+ *
+ *
+ *
+ * @param vDataSet
+ */
+ public void addDataSet(uk.ac.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetList.addElement(vDataSet);
+ } //-- void addDataSet(uk.ac.vamsas.objects.core.DataSet)
+
+ /**
+ * Method addDataSet
+ *
+ *
+ *
+ * @param index
+ * @param vDataSet
+ */
+ public void addDataSet(int index, uk.ac.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetList.insertElementAt(vDataSet, index);
+ } //-- void addDataSet(int, uk.ac.vamsas.objects.core.DataSet)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param vTree
+ */
+ public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.addElement(vTree);
+ } //-- void addTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.DataSet getDataSet(int)
+
+ /**
+ * Method getDataSet
+ *
+ *
+ *
+ * @return DataSet
+ */
+ public uk.ac.vamsas.objects.core.DataSet[] getDataSet()
+ {
+ int size = _dataSetList.size();
+ uk.ac.vamsas.objects.core.DataSet[] mArray = new uk.ac.vamsas.objects.core.DataSet[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.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 (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree[] getTree()
+ {
+ int size = _treeList.size();
+ uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ }
+ return mArray;
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.DataSet removeDataSet(int index)
+ {
+ java.lang.Object obj = _dataSetList.elementAt(index);
+ _dataSetList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.DataSet) obj;
+ } //-- uk.ac.vamsas.objects.core.DataSet removeDataSet(int)
+
+ /**
+ * Method removeTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTree(int index)
+ {
+ java.lang.Object obj = _treeList.elementAt(index);
+ _treeList.removeElementAt(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ } //-- uk.ac.vamsas.objects.core.Tree removeTree(int)
+
+ /**
+ * Method setDataSet
+ *
+ *
+ *
+ * @param index
+ * @param vDataSet
+ */
+ public void setDataSet(int index, uk.ac.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, uk.ac.vamsas.objects.core.DataSet)
+
+ /**
+ * Method setDataSet
+ *
+ *
+ *
+ * @param dataSetArray
+ */
+ public void setDataSet(uk.ac.vamsas.objects.core.DataSet[] dataSetArray)
+ {
+ //-- copy array
+ _dataSetList.removeAllElements();
+ for (int i = 0; i < dataSetArray.length; i++) {
+ _dataSetList.addElement(dataSetArray[i]);
+ }
+ } //-- void setDataSet(uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param treeArray
+ */
+ public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
+ {
+ //-- copy array
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
+ }
+ } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return VAMSAS
+ */
+ public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VAMSAS.class, reader);
+ } //-- uk.ac.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:VAMSASDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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 uk.ac.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 uk.ac.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();
+ } //-- uk.ac.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 uk.ac.vamsas.objects.core.LockFile getLockFile()
+ {
+ return this._lockFile;
+ } //-- uk.ac.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(uk.ac.vamsas.objects.core.LockFile lockFile)
+ {
+ this._lockFile = lockFile;
+ } //-- void setLockFile(uk.ac.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 uk.ac.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VamsasDocument.class, reader);
+ } //-- uk.ac.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:VamsasDocumentDescriptor.java 264 2006-12-14 17:42:54Z JimP $
+ */
+
+package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ */
+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(uk.ac.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( (uk.ac.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 uk.ac.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);
+ } //-- uk.ac.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 uk.ac.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