+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.client.objects;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class SequenceSet.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceSet extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _gapChar
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
+ * Field _sequenceList
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _sequenceSetAnnotationsList
+ */
+ private java.util.Vector _sequenceSetAnnotationsList;
+
+ /**
+ * Field _alignmentList
+ */
+ private java.util.Vector _alignmentList;
+
+ /**
+ * Field _tree
+ */
+ private org.vamsas.client.objects.Tree _tree;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.client.objects.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet()
+ {
+ super();
+ _sequenceList = new Vector();
+ _sequenceSetAnnotationsList = new Vector();
+ _alignmentList = new Vector();
+ } //-- org.vamsas.client.objects.SequenceSet()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param vAlignment
+ */
+ public void addAlignment(org.vamsas.client.objects.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.addElement(vAlignment);
+ } //-- void addAlignment(org.vamsas.client.objects.Alignment)
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param index
+ * @param vAlignment
+ */
+ public void addAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.insertElementAt(vAlignment, index);
+ } //-- void addAlignment(int, org.vamsas.client.objects.Alignment)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param vSequence
+ */
+ public void addSequence(org.vamsas.client.objects.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.addElement(vSequence);
+ } //-- void addSequence(org.vamsas.client.objects.Sequence)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void addSequence(int index, org.vamsas.client.objects.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.insertElementAt(vSequence, index);
+ } //-- void addSequence(int, org.vamsas.client.objects.Sequence)
+
+ /**
+ * Method addSequenceSetAnnotations
+ *
+ *
+ *
+ * @param vSequenceSetAnnotations
+ */
+ public void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
+ } //-- void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
+
+ /**
+ * Method addSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSetAnnotations
+ */
+ public void addSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
+ } //-- void addSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
+
+ /**
+ * Method deleteAligned
+ *
+ */
+ public void deleteAligned()
+ {
+ this._has_aligned= false;
+ } //-- void deleteAligned()
+
+ /**
+ * Method enumerateAlignment
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAlignment()
+ {
+ return _alignmentList.elements();
+ } //-- java.util.Enumeration enumerateAlignment()
+
+ /**
+ * Method enumerateSequence
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateSequence()
+ {
+ return _sequenceList.elements();
+ } //-- java.util.Enumeration enumerateSequence()
+
+ /**
+ * Method enumerateSequenceSetAnnotations
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateSequenceSetAnnotations()
+ {
+ return _sequenceSetAnnotationsList.elements();
+ } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof SequenceSet) {
+
+ SequenceSet temp = (SequenceSet)obj;
+ if (this._gapChar != null) {
+ if (temp._gapChar == null) return false;
+ else if (!(this._gapChar.equals(temp._gapChar)))
+ return false;
+ }
+ else if (temp._gapChar != null)
+ return false;
+ if (this._aligned != temp._aligned)
+ return false;
+ if (this._has_aligned != temp._has_aligned)
+ return false;
+ if (this._sequenceList != null) {
+ if (temp._sequenceList == null) return false;
+ else if (!(this._sequenceList.equals(temp._sequenceList)))
+ return false;
+ }
+ else if (temp._sequenceList != null)
+ return false;
+ if (this._sequenceSetAnnotationsList != null) {
+ if (temp._sequenceSetAnnotationsList == null) return false;
+ else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
+ return false;
+ }
+ else if (temp._sequenceSetAnnotationsList != null)
+ return false;
+ if (this._alignmentList != null) {
+ if (temp._alignmentList == null) return false;
+ else if (!(this._alignmentList.equals(temp._alignmentList)))
+ return false;
+ }
+ else if (temp._alignmentList != null)
+ return false;
+ if (this._tree != null) {
+ if (temp._tree == null) return false;
+ else if (!(this._tree.equals(temp._tree)))
+ return false;
+ }
+ else if (temp._tree != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return boolean
+ * @return the value of field 'aligned'.
+ */
+ public boolean getAligned()
+ {
+ return this._aligned;
+ } //-- boolean getAligned()
+
+ /**
+ * Method getAlignment
+ *
+ *
+ *
+ * @param index
+ * @return Alignment
+ */
+ public org.vamsas.client.objects.Alignment getAlignment(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentList.size())) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
+ }
+
+ return (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
+ } //-- org.vamsas.client.objects.Alignment getAlignment(int)
+
+ /**
+ * Method getAlignment
+ *
+ *
+ *
+ * @return Alignment
+ */
+ public org.vamsas.client.objects.Alignment[] getAlignment()
+ {
+ int size = _alignmentList.size();
+ org.vamsas.client.objects.Alignment[] mArray = new org.vamsas.client.objects.Alignment[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.client.objects.Alignment[] getAlignment()
+
+ /**
+ * Method getAlignmentAsReference
+ *
+ * Returns a reference to 'alignment'. No type checking is
+ * performed on any modications to the Vector.
+ *
+ * @return Vector
+ * @return returns a reference to the Vector.
+ */
+ public java.util.Vector getAlignmentAsReference()
+ {
+ return _alignmentList;
+ } //-- java.util.Vector getAlignmentAsReference()
+
+ /**
+ * Method getAlignmentCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentCount()
+ {
+ return _alignmentList.size();
+ } //-- int getAlignmentCount()
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return String
+ * @return the value of field 'gapChar'.
+ */
+ public java.lang.String getGapChar()
+ {
+ return this._gapChar;
+ } //-- java.lang.String getGapChar()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.client.objects.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.client.objects.Provenance getProvenance()
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @param index
+ * @return Sequence
+ */
+ public org.vamsas.client.objects.Sequence getSequence(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceList.size())) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
+ }
+
+ return (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
+ } //-- org.vamsas.client.objects.Sequence getSequence(int)
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @return Sequence
+ */
+ public org.vamsas.client.objects.Sequence[] getSequence()
+ {
+ int size = _sequenceList.size();
+ org.vamsas.client.objects.Sequence[] mArray = new org.vamsas.client.objects.Sequence[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.client.objects.Sequence[] getSequence()
+
+ /**
+ * Method getSequenceAsReference
+ *
+ * Returns a reference to 'sequence'. No type checking is
+ * performed on any modications to the Vector.
+ *
+ * @return Vector
+ * @return returns a reference to the Vector.
+ */
+ public java.util.Vector getSequenceAsReference()
+ {
+ return _sequenceList;
+ } //-- java.util.Vector getSequenceAsReference()
+
+ /**
+ * Method getSequenceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSequenceCount()
+ {
+ return _sequenceList.size();
+ } //-- int getSequenceCount()
+
+ /**
+ * Method getSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
+ throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
+ }
+
+ return (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
+ } //-- org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int)
+
+ /**
+ * Method getSequenceSetAnnotations
+ *
+ *
+ *
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
+ {
+ int size = _sequenceSetAnnotationsList.size();
+ org.vamsas.client.objects.SequenceSetAnnotations[] mArray = new org.vamsas.client.objects.SequenceSetAnnotations[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
+
+ /**
+ * Method getSequenceSetAnnotationsAsReference
+ *
+ * Returns a reference to 'sequenceSetAnnotations'. No type
+ * checking is performed on any modications to the Vector.
+ *
+ * @return Vector
+ * @return returns a reference to the Vector.
+ */
+ public java.util.Vector getSequenceSetAnnotationsAsReference()
+ {
+ return _sequenceSetAnnotationsList;
+ } //-- java.util.Vector getSequenceSetAnnotationsAsReference()
+
+ /**
+ * Method getSequenceSetAnnotationsCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSequenceSetAnnotationsCount()
+ {
+ return _sequenceSetAnnotationsList.size();
+ } //-- int getSequenceSetAnnotationsCount()
+
+ /**
+ * Returns the value of field 'tree'.
+ *
+ * @return Tree
+ * @return the value of field 'tree'.
+ */
+ public org.vamsas.client.objects.Tree getTree()
+ {
+ return this._tree;
+ } //-- org.vamsas.client.objects.Tree getTree()
+
+ /**
+ * Method hasAligned
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasAligned()
+ {
+ return this._has_aligned;
+ } //-- boolean hasAligned()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAlignment
+ *
+ *
+ *
+ * @param index
+ * @return Alignment
+ */
+ public org.vamsas.client.objects.Alignment removeAlignment(int index)
+ {
+ java.lang.Object obj = _alignmentList.elementAt(index);
+ _alignmentList.removeElementAt(index);
+ return (org.vamsas.client.objects.Alignment) obj;
+ } //-- org.vamsas.client.objects.Alignment removeAlignment(int)
+
+ /**
+ * Method removeAllAlignment
+ *
+ */
+ public void removeAllAlignment()
+ {
+ _alignmentList.removeAllElements();
+ } //-- void removeAllAlignment()
+
+ /**
+ * Method removeAllSequence
+ *
+ */
+ public void removeAllSequence()
+ {
+ _sequenceList.removeAllElements();
+ } //-- void removeAllSequence()
+
+ /**
+ * Method removeAllSequenceSetAnnotations
+ *
+ */
+ public void removeAllSequenceSetAnnotations()
+ {
+ _sequenceSetAnnotationsList.removeAllElements();
+ } //-- void removeAllSequenceSetAnnotations()
+
+ /**
+ * Method removeSequence
+ *
+ *
+ *
+ * @param index
+ * @return Sequence
+ */
+ public org.vamsas.client.objects.Sequence removeSequence(int index)
+ {
+ java.lang.Object obj = _sequenceList.elementAt(index);
+ _sequenceList.removeElementAt(index);
+ return (org.vamsas.client.objects.Sequence) obj;
+ } //-- org.vamsas.client.objects.Sequence removeSequence(int)
+
+ /**
+ * Method removeSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
+ {
+ java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
+ _sequenceSetAnnotationsList.removeElementAt(index);
+ return (org.vamsas.client.objects.SequenceSetAnnotations) obj;
+ } //-- org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int)
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(boolean aligned)
+ {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ } //-- void setAligned(boolean)
+
+ /**
+ * Method setAlignment
+ *
+ *
+ *
+ * @param index
+ * @param vAlignment
+ */
+ public void setAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentList.size())) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
+ }
+ _alignmentList.setElementAt(vAlignment, index);
+ } //-- void setAlignment(int, org.vamsas.client.objects.Alignment)
+
+ /**
+ * Method setAlignment
+ *
+ *
+ *
+ * @param alignmentArray
+ */
+ public void setAlignment(org.vamsas.client.objects.Alignment[] alignmentArray)
+ {
+ //-- copy array
+ _alignmentList.removeAllElements();
+ for (int i = 0; i < alignmentArray.length; i++) {
+ _alignmentList.addElement(alignmentArray[i]);
+ }
+ } //-- void setAlignment(org.vamsas.client.objects.Alignment)
+
+ /**
+ * Method setAlignment
+ *
+ * Sets the value of 'alignment' by copying the given Vector.
+ *
+ * @param alignmentVector the Vector to copy.
+ */
+ public void setAlignment(java.util.Vector alignmentVector)
+ {
+ //-- copy vector
+ _alignmentList.removeAllElements();
+ for (int i = 0; i < alignmentVector.size(); i++) {
+ _alignmentList.addElement((org.vamsas.client.objects.Alignment)alignmentVector.elementAt(i));
+ }
+ } //-- void setAlignment(java.util.Vector)
+
+ /**
+ * Method setAlignmentAsReference
+ *
+ * Sets the value of 'alignment' by setting it to the given
+ * Vector. No type checking is performed.
+ *
+ * @param alignmentVector the Vector to copy.
+ */
+ public void setAlignmentAsReference(java.util.Vector alignmentVector)
+ {
+ _alignmentList = alignmentVector;
+ } //-- void setAlignmentAsReference(java.util.Vector)
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar the value of field 'gapChar'.
+ */
+ public void setGapChar(java.lang.String gapChar)
+ {
+ this._gapChar = gapChar;
+ } //-- void setGapChar(java.lang.String)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.client.objects.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.client.objects.Provenance)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void setSequence(int index, org.vamsas.client.objects.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceList.size())) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
+ }
+ _sequenceList.setElementAt(vSequence, index);
+ } //-- void setSequence(int, org.vamsas.client.objects.Sequence)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param sequenceArray
+ */
+ public void setSequence(org.vamsas.client.objects.Sequence[] sequenceArray)
+ {
+ //-- copy array
+ _sequenceList.removeAllElements();
+ for (int i = 0; i < sequenceArray.length; i++) {
+ _sequenceList.addElement(sequenceArray[i]);
+ }
+ } //-- void setSequence(org.vamsas.client.objects.Sequence)
+
+ /**
+ * Method setSequence
+ *
+ * Sets the value of 'sequence' by copying the given Vector.
+ *
+ * @param sequenceVector the Vector to copy.
+ */
+ public void setSequence(java.util.Vector sequenceVector)
+ {
+ //-- copy vector
+ _sequenceList.removeAllElements();
+ for (int i = 0; i < sequenceVector.size(); i++) {
+ _sequenceList.addElement((org.vamsas.client.objects.Sequence)sequenceVector.elementAt(i));
+ }
+ } //-- void setSequence(java.util.Vector)
+
+ /**
+ * Method setSequenceAsReference
+ *
+ * Sets the value of 'sequence' by setting it to the given
+ * Vector. No type checking is performed.
+ *
+ * @param sequenceVector the Vector to copy.
+ */
+ public void setSequenceAsReference(java.util.Vector sequenceVector)
+ {
+ _sequenceList = sequenceVector;
+ } //-- void setSequenceAsReference(java.util.Vector)
+
+ /**
+ * Method setSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSetAnnotations
+ */
+ public void setSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
+ throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
+ }
+ _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
+ } //-- void setSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
+
+ /**
+ * Method setSequenceSetAnnotations
+ *
+ *
+ *
+ * @param sequenceSetAnnotationsArray
+ */
+ public void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
+ {
+ //-- copy array
+ _sequenceSetAnnotationsList.removeAllElements();
+ for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
+ _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
+ }
+ } //-- void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
+
+ /**
+ * Method setSequenceSetAnnotations
+ *
+ * Sets the value of 'sequenceSetAnnotations' by copying the
+ * given Vector.
+ *
+ * @param sequenceSetAnnotationsVector the Vector to copy.
+ */
+ public void setSequenceSetAnnotations(java.util.Vector sequenceSetAnnotationsVector)
+ {
+ //-- copy vector
+ _sequenceSetAnnotationsList.removeAllElements();
+ for (int i = 0; i < sequenceSetAnnotationsVector.size(); i++) {
+ _sequenceSetAnnotationsList.addElement((org.vamsas.client.objects.SequenceSetAnnotations)sequenceSetAnnotationsVector.elementAt(i));
+ }
+ } //-- void setSequenceSetAnnotations(java.util.Vector)
+
+ /**
+ * Method setSequenceSetAnnotationsAsReference
+ *
+ * Sets the value of 'sequenceSetAnnotations' by setting it to
+ * the given Vector. No type checking is performed.
+ *
+ * @param sequenceSetAnnotationsVector the Vector to copy.
+ */
+ public void setSequenceSetAnnotationsAsReference(java.util.Vector sequenceSetAnnotationsVector)
+ {
+ _sequenceSetAnnotationsList = sequenceSetAnnotationsVector;
+ } //-- void setSequenceSetAnnotationsAsReference(java.util.Vector)
+
+ /**
+ * Sets the value of field 'tree'.
+ *
+ * @param tree the value of field 'tree'.
+ */
+ public void setTree(org.vamsas.client.objects.Tree tree)
+ {
+ this._tree = tree;
+ } //-- void setTree(org.vamsas.client.objects.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceSet
+ */
+ public static org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.client.objects.SequenceSet) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSet.class, reader);
+ } //-- org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}